"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language" "Bioengineering","telatin/seqfu2","screenshots.md",".md","2336","97","# Seqfu splash screens ## count ![`seqfu count --help`](docs/img/screenshot-count.png ""SeqFu count"") ## stats ![`seqfu stats --help`](docs/img/screenshot-stats.png ""SeqFu stats"") ## derep ![`seqfu derep --help`](docs/img/screenshot-derep.png ""SeqFu derep"") ## interleave ![`seqfu interleave --help`](docs/img/screenshot-interleave.png ""SeqFu interleave"") ## deinterleave ![`seqfu deinterleave --help`](docs/img/screenshot-deinterleave.png ""SeqFu deinterleave"") ## metadata ![`seqfu metadata --help`](docs/img/screenshot-metadata.png ""SeqFu metadata"") ## cat ![`seqfu cat --help`](docs/img/screenshot-cat.png ""SeqFu cat"") ## grep ![`seqfu grep --help`](docs/img/screenshot-grep.png ""SeqFu grep"") ## head ![`seqfu head --help`](docs/img/screenshot-head.png ""SeqFu head"") ## tail ![`seqfu tail --help`](docs/img/screenshot-tail.png ""SeqFu tail"") ## view ![`seqfu view --help`](docs/img/screenshot-view.png ""SeqFu view"") ![`seqfu view data/primers/small.fq -o CCTACGGGAG -r ATGAGCGTCTCG`](docs/img/screenshot-view-example.png ""SeqFu view example"") seqfu view data/qualities.fq ![`seqfu view data/qualities.fq`](docs/img/screenshot-view-qual.png ""SeqFu view qualities"") seqfu view --ascii data/qualities.fq ![`seqfu view --ascii data/qualities.fq`](docs/img/screenshot-view-qual-ascii.png ""SeqFu view qualities"") seqfu view --qual-chars data/qualities.fq ![`seqfu view --qual-chars data/qualities.fq`](docs/img/screenshot-view-raw.png ""SeqFu view encoded quality"") ## rc ![`seqfu rc --help`](docs/img/screenshot-rc.png ""SeqFu rc"") ## tab ![`seqfu tab --help`](docs/img/screenshot-tab.png ""SeqFu tab"") ## lanes ![`seqfu lanes --help`](docs/img/screenshot-lanes.png ""SeqFu lanes"") ## rotate ![`seqfu rotate --help`](docs/img/screenshot-rotate.png ""SeqFu rotate"") ## fu-orf ![`fu-orf --help`](docs/img/screenshot-fu-orf.png ""SeqFu fu-orf"") ## fu-nanotags ![`fu-nanotags --help`](docs/img/screenshot-fu-nanotags.png ""SeqFu fu-nanotags"") ## fu-split ![`pwd && find .. -name ""msa.*""`](docs/img/screenshot-ls.png ""Find MSA"") ## fu-split ![`fu-split --help`](docs/img/screenshot-fu-split.png ""SeqFu split"") ## fu-msa ![`fu-msa ./data/msa.fa --screenshot`](docs/img/screenshot-fu-msa-1.png ""SeqFu MSA viewer"") ![`fu-msa ./data/msa.faa --screenshot`](docs/img/screenshot-fu-msa-2.png ""SeqFu MSA viewer"") ","Markdown" "Bioengineering","telatin/seqfu2","re/gettable.R",".R","654","30","#!/usr/bin/env RScript url = ""https://en.wikipedia.org/wiki/List_of_restriction_enzyme_cutting_sites:_Ba-Bc#Whole_list_navigation"" args <- commandArgs(TRUE) if (length(args) != 2) { stop(""Missing argument: URL OutputFile\n"") } url <- args[[1]] output <- args[[2]] library(tidyverse) library(rvest) html = read_html(url) tables = html %>% html_nodes(css = ""table"") filt = tables %>% html_nodes(css = ""sortable"") %>% html_table(fill = TRUE) View(tables) table <- tables[ -c(2:3) ] colnames(table) <- c(""enzyme"", ""source"", ""seq"", ""cut"", ""isoschizomers"") table$enzyme <- sub(""\\[.+\\]"", """", table$enzyme) write.csv(table, output) ","R" "Bioengineering","telatin/seqfu2","re/Ba-Bc.md",".md","10857","59","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:---------|:--------------------------------|:-----------------------|------:|:------------------------------------------------------------------------------------------------------| | Bac36I | Bacillus alcalophilus 36 | GGNCC | 1 | AspS9I, AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV | | BalI | Brevibacterium albidum | TGGCCA | 3 | | | Bal228I | Bacillus alcalophilus 228 | GGNCC | 1 | AspS9I, AvcI, BavAII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | | BamHI | Bacillus amyloliquefaciens H | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, Bce751I, Bsp98I, Bsp4009I, BspAAIII, CelI, Nsp29132II, NspSAIV, SolI, SurI | | BamNII | Bacillus amyloliquefaciens N | GGWCC | 1 | BcuAI, BsrAI, CauI, EagMI, FdiI, HgiCII, HgiJI, SinI | | BanI | Bacillus aneurinolyticus | GGYRCC | 1 | AccB1I, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BanII | Bacillus aneurinolyticus | GRGCYC | 5 | | | BanIII | Bacillus aneurinolyticus | ATCGAT | 2 | AagI, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | | BanAI | Bacillus anthracis | GGCC | 2 | | | BauI | Bacillus aquaemaris RFL1 | CACGAG | 1 | | | BavI | Bacillus alvei | CAGCTG | 3 | | | BavAI | Bacillus alvei A | CAGCTG | 3 | | | BavAII | Bacillus alvei A | GGNCC | 1 | AspS9I, AvcI, BavBII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | | BavBI | Bacillus alvei B | CAGCTG | 3 | | | BavBII | Bacillus alvei B | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, Bsu54I, FmuI, Pde12I | | BavCI | Bacillus alvei C | ATCGAT | 2 | AagI, BanIII, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | | BbeI | Bifidobacterium breve YIT4006 | GGCGCC | 5 | | | BbiII | Bifidobacterium bifidum YIT4007 | GRCGYC | 2 | AcyI, AhaII, BbiII, HgiHII, Hin1I, Hsp92I, Msp17I, PamII | | Bbi24I | Bifidobacterium bifidum S-24 | ACGCGT | 1 | | | BbrI | Bordetella bronchiseptica 4994 | AAGCTT | 1 | | | Bbr7I | Bacillus brevis 7 | GAAGAC | 9 | | | BbrPI | Bacillus brevis | CACGTG | 3 | AcvI, BcoAI, Eco72I, PmaCI, PmlI, PspCI | | BbsI | Bacillus laterosporus | GAAGAC | 8 | | | BbuI | Bacillus circulans | GCATGC | 5 | | | BbvI | Bacillus brevis | GCAGC | 8 | AlwXI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | | BbvII | Bacillus brevis 80 | GAAGAC | 8 | | | Bbv12I | Bacillus brevis 12 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | | Bbv16II | Bacillus brevis 16 | GAAGAC | 8 | | | BbvAII | Bacillus brevis A | ATCGAT | 2 | BavCI, Bci29I, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | | BbvAIII | Bacillus brevis A | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Bsu23I, Kpn2I | | BbvBI | Bacillus brevis B | GGYRCC | 1 | BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BbvCI | Bacillus brevis | CCTCAGC | 2 | AbeI | | Bca77I | Bacillus caldolyticus | WCCGGW | 1 | | | BccI | Bacteroides caccae | CCATC | 9 | | | Bce22I | Bacillus cereus 22 | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, FmuI, Pde12I | | Bce83I | Bacillus cereus 83 | CTTGAG | 12 | | | Bce243I | Bacillus cereus | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | | Bce751I | Bacillus cereus 751 | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, Bsp4009I, BstI, NspSAIV, Pfl8I | | BceAI | Bacillus cereus 1315 | ACGGC | 9 | | | BceBI | Bacillus cereus 1323 | CGCG | 2 | AccII, Bsh1236I, BtkI, Csp68KVI, FalII, FauBII, FnuDII, SelI, ThaI | | BcefI | Bacillus cereus fluorescens | ACGGC | 10 | | | Bci29I | Bacillus circulans 29 | ATCGAT | 2 | BavCI, BciBI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | | BciBI | Bacillus circulans B | ATCGAT | 2 | BavCI, BcmI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | | BciBII | Bacillus circulans B | CCWGG | 2 | AjnI, ApyI, BptI, Bst1I, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | | BciVI | Bacillus circulans | GTATCC | 10 | BfuI | | BclI | Bacillus caldolyticus | TGATCA | 1 | AbaI, BsiQI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | | BcmI | Bacillus sp. | ATCGAT | 2 | BsuTUI, Bsu15I, BavCI, Bli86I, BspZEI, Rme21I, BseCI, BdiI | | BcnI | Bacillus centrosporus RFL1 | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, Eco1831I, HgiS22I,Kpn49kII, NciI | | BcoI | Bacillus coagulans SM 1 | CYCGRG | 1 | Ama87I, AquI, BsoBI, BstSI, Eco88I, NspSAI, OfoI, PunAI | | Bco5I | Bacillus coagulans 5 | CTCTTC | 7 | | | Bco27I | Bacillus coagulans 27 | CCGG | 1 | | | Bco116I | Bacillus coagulans 116 | CTCTTC | 7 | | | Bco118I | Bacillus coagulans 118 | RCCGGY | 1 | | | BcoAI | Bacillus coagulans AUCM B-732 | CACGTG | 3 | AcvI, BbrPI, Eco72I, PmaCI, PmlI, PspCI | | BcoKI | Bacillus coagulans | CTCTTC | 7 | | | BcuI | Bacillus coagulans Vs 29-022 | ACTAGT | 1 | AhII, AclNI, SpeI | | BcuAI | Bacillus cereus BKM B-814 | GGWCC | 1 | BamNxI, BsrAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI |","Markdown" "Bioengineering","telatin/seqfu2","re/E-F.md",".md","16628","109","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:---------|:-----------------------------------|:-----------------------|------:|:-------------------------------------------------------------------| | EacI | Eubacterium acidaminophilum | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI, BstH9I,  Bst31TI, Bth617I, Ral8I | | EaeI | Enterobacter aerogenes | YGGCCR | 1 | | | Eae46I | Enterobacter aerogenes 46 | CCGCGG | 4 | | | EaeAI | Enterobacter aerogenes | CCCGGG | 1 | AhyI, Cfr9I, EclRI, PaeBI, PspAI, PspALI, XcyI, XmaI, XmaCI | | EagI | Enterobacter agglomerans | CGGCCG | 1 | AaaI, BseX3I, BstZI, EclXI, Eco52I, SenPT16I, XmaIII | | EagBI | Enterobacter agglomerans CBNU45 | CGATCG | 4 | Afa16RI, Afa22MI, BspCI, ErhB9I, NblI, Psu161I, RshI, XorII | | EagMI | Enterobacter agglomerans M3 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | | Eam1104I | Enterobacter amnigenus RFL1104 | CTCTTC | 7 | | | EarI | Enterobacter aerogenes | CTCTTC | 7 | | | EcaI | Enterobacter cloacae | GGTNACC | 1 | AcrII, Bse64I, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | | EciI | Escherichia coli | GGCGGA | 11 | | | Eci125I | Escherichia coli VKM-125 | GGTNACC | 1 | AcrII, AspAI, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | | EclI | Enterobacter cloacae | CAGCTG | 3 | | | Ecl136II | Enterobacter cloacae RFL136 | GAGCTC | 3 | | | EclRI | Enterobacter cloacae R | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, Pac25I, PspAI, PspALI, XcyI, XmaI, XmaCI | | EclXI | Enterobacter cloacae 590 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, Eco52I, SenPT16I, XmaIII | | Ecl18kI | Enterobacter cloacae 18k | CCNGG | 1 | | | Ecl37kI | Enterobacter cloacae 37k | CTGCAG | 5 | AjoI, AliAJI, Ecl2zI, PaePI, Psp23I, PstI, Sag16I, SflI, YenI | | Ecl2zI | Enterobacter cloacae 2z | CTGCAG | 5 | AliAJI, Bsp63I, CfrA4I, PaePI, Pfl21I, PstI, SflI, Sst12I, YenI | | Eco24I | Escherichia coli RFL24 | GRGCYC | 5 | | | Eco31I | Escherichia coli RFL31 | GGTCTC | 7 | | | Eco32I | Escherichia coli RFL32 | GATATC | 3 | | | Eco47I | Escherichia coli RFL47 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | | Eco47III | Escherichia coli RFL47 | AGCGCT | 3 | AfeI, AitI, Aor51H, FunI | | Eco52I | Escherichia coli RFL52 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, SenPT16I, XmaIII | | Eco56I | Escherichia coli RFL56 | GCCGGC | 1 | | | Eco57I | Escherichia coli RFL57 | CTGAAG | 13 | AcuI, BspKT5I | | Eco64I | Escherichia coli RFL64 | GGYRCC | 1 | BanI, BbvBI, BspT107I, BshNI, HgiCI, HgiHI, MspB4I, PfaAI | | Eco72I | Escherichia coli RFL72 | CACGTG | 3 | AcvI, BcoAI, BbrPI, PmaCI, PmlI, PspCI | | Eco78I | Escherichia coli RFL78 | GGCGCC | 3 | | | Eco81I | Escherichia coli RFL81 | CCTNAGG | 2 | AxyI, Bse21I, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | | Eco88I | Escherichia coli RFL88 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BstSI, Eco27kI, NspSAI, PlaAI, PunAI | | Eco91I | Escherichia coli RFL91 | GGTNACC | 1 | Bse64I, BstEII, BstPI, BstT9I, BstT10I, EcaI, Eci125I, NspSAII | | Eco105I | Escherichia coli RFL105 | TACGTA | 3 | | | Eco130I | Escherichia coli RFL130 | CCWWGG | 1 | | | Eco147I | Escherichia coli RFL147 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | | Eco255I | Escherichia coli RFL255 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, RflFII, ScaI, ZrmI | | Eco1831I | Escherichia coli RFL1831 | CCSGG | 1 | AhaI, AseII, AsuC2I, BcnI,  BpuMI, CauII, EcoHI, HgiS22I | | EcoA4I | Escherichia coli A4 | GGTCTC | 7 | | | EcoHI | Escherichia coli HI | CCSGG | 1 | AsuC2I, BcnI, BpuMI, CauII, EcoHI, HgiS22I, Kpn49kII, NciI | | EcoHK31I | Escherichia coli HK31 | YGGCCR | 1 | | | EcoICRI | Escherichia coli 2bT | GAGCTC | 3 | | | Eco75KI | Escherichia coli BKM | GRGCYC | 5 | | | Eco57MI | Escherichia coli RFL57M | CTGRAG | 13 | | | EcoO44I | Escherichia coli O44 Hiromi | GGTCTC | 7 | | | EcoO65I | Escherichia coli K11a | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstPI, BstT9I, EcaI, Eco91I, EcoO128I | | EcoO109I | Escherichia coli H709c | RGGNCCY | 2 | | | EcoO128I | Escherichia coli O128Ly3 | GGTNACC | 1 | AspAI, Bse64I, BstEII, BstT9I, EcaI, EcoO65I, NspSAII, PspEI | | EcoP15I | Escherichia coli P15 | CAGCAG | 11 | | | EcoRI | Escherichia coli RY13 | GAATTC | 1 | | | EcoRII | Escherichia coli R245 | CCWGG | 1 | ApaORI, BseBI, BspNI, BstNI, BstOI, Bst2UI, MvaI, SspAI, ZanI | | EcoRV | Escherichia coli J62 pLG74 | GATATC | 3 | | | EcoT14I | Escherichia coli TB14 | CCWWGG | 1 | | | EcoT22I | Escherichia coli TB22 | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SepI, SspD5II | | EcoT38I | Escherichia coli TH38 | GRGCYC | 5 | | | EcoVIII | Escherichia coli E1585-68 | AAGCTT | 1 | | | Eco13kI | Escherichia coli 13k | CCNGG | 1 | | | Eco21kI | Escherichia coli 21k | CCNGG | 1 | | | Eco27kI | Escherichia coli 27 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, OfoI, PunAI | | Eco29kI | Escherichia coli | CCGCGG | 4 | | | Eco53kI | Escherichia coli 53k | GAGCTC | 3 | | | Eco137kI | Escherichia coli 137k | CCNGG | 1 | | | EgeI | Enterobacter gergoviae NA | GGCGCC | 3 | | | EheI | Erwinia herbicola 9/5 | GGCGCC | 3 | | | ErhI | Erwinia rhaponici B9 | CCWWGG | 1 | | | ErhB9I | Erwinia rhaponici B9 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, NblI, Ple19I, Psu161I, RshI, XorII | | ErhB9II | Erwinia rhaponici B9 | CCWWGG | 1 | | | ErpI | Erwinia rhaponici | GGWCC | 1 | Bme18I, BthAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | | EsaBC3I | Environmental sample BC3 | TCGA | 2 | | | EsaBC4I | Environmental sample BC4 | GGCC | 2 | | | EspI | Eucapsis sp. | GCTNAGC | 2 | | | Esp3I | Erwinia sp. RFL3 | CGTCTC | 7 | | | Esp4I | Erwinia sp. RFL4 | CTTAAG | 1 | | | FalII | Flavobacterium aquatile Ob10 | CGCG | 2 | BepI, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, FalII, SelI, ThaI | | FaqI | Flavobacterium aquatile RFL1 | GGGAC | 9 | | | FatI | Flavobacterium aquatile NL3 | CATG | 1 | | | FauI | Flavobacterium aquatile | CCCGC | 9 | | | FauBII | Flavobacterium aureus B | CGCG | 2 | Bpu95I, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, Csp68KVI, SelI, ThaI | | FauNDI | Flavobacterium aquatile ND | CATATG | 2 | | | FbaI | Flavobacterium balustinum | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, Ksp22I,  ParI | | FblI | Flavobacterium balustinum | GTMKAC | 2 | AccI, XmiI | | FbrI | Flavobacterium breve | GCNGC | 2 | | | FdiI | Fremyella diplosiphon | GGWCC | 1 | Bme18I, BthAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | | FdiII | Fremyella diplosiphon | TGCGCA | 3 | Acc16I, AosI, AviII, FspI, MstI, NsbI, PamI, Pun14627I | | FgoI | Fervidobacterium gondwanense AB39T | CTAG | 1 | | | FmuI | Flavobacterium multivorum | GGNCC | 4 | FmuI AvcI, BavAII, Bce22I, Bsu54I, NspIV, Pde12I, UnbI | | FnuAI | Fusobacterium nucleatum A | GANTC | 1 | | | FnuCI | Fusobacterium nucleatum C | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuEI, MgoI, NphI, SauMI | | FnuDI | Fusobacterium nucleatum D | GGCC | 2 | | | FnuDII | Fusobacterium nucleatum D | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FnuDII, ThaI | | FnuDIII | Fusobacterium nucleatum D | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, HhaI, Hin6I, HinP1I, HspAI, SciNI | | FnuEI | Fusobacterium nucleatum E | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, Sau3AI | | Fnu4HI | Fusobacterium nucleatum 4H | GCNGC | 2 | | | FokI | Flavobacterium okeanokoites | GGATG | 8 | | | FriOI | Flavobacterium sp. O9 | GRGCYC | 5 | | | FseI | Frankia sp. Eu11b | GGCCGGCC | 6 | | | FsiI | Frankia sp. | RAATTY | 1 | AcsI, ApoI,  CfaI, XapI | | FspI | Fischerella sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, MstI, NsbI, PamI, Pun14627I | | FspII | Fischerella sp. | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, Ssp1I, SviI | | Fsp1604I | Flavobacterium sp. I 16-04 | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, SleI | | FspAI | Flexibacter sp. TV-m21K | RTGCGCAY | 4 | | | FspBI | Flavobacterium sp. RFLI | CTAG | 1 | | | Fsp4HI | Flavobacterium sp. 4H | GCNGC | 2 | | | FspMSI | Fischerella sp. | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, HgiBI, HgiEI, Kzo49I, SmuEI | | FssI | Fibrobacter succinogenes S85 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Kzo49I, VpaK11AI | | FunI | Fischerella uniformis | AGCGCT | 3 | AfeI, AitI, Aor51H, Eco47III | | FunII | Fischerella uniformis | GAATTC | 1 | |","Markdown" "Bioengineering","telatin/seqfu2","re/T-Z.md",".md","10769","69","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:--------------|:----------------------------------|:-----------------------|------:|:-------------------------------------------------------------------| | TaaI | Thermus aquaticus Vn 4-311 | ACNGT | 3 | | | TaiI | Thermus aquaticus cs1-331 | ACGT | 4 | | | TaqI | Thermus aquaticus | TCGA | 1 | | | TaqII | Thermus aquaticus YTI | GACCGA | 11 | | | Taq52I | Thermus aquaticus YS52 | GCWGC | 1 | AceI, ApeKI, SuiI, TseI | | TaqXI | Thermus aquaticus | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, MvaI, SleI, SspAI | | TasI | Thermus aquaticus Vn 4-211 | AATT | 1 | | | TatI | Thermus aquaticus CBA1-331 | WGTACW | 1 | | | TauI | Thermus aquaticus | GCSGC | 4 | | | TelI | Tolypothrix elabens | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, Tth111I | | TfiI | Thermus filiformis | GAWTC | 1 | | | ThaI | Thermoplasma acidophilum | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FalII, FnuDII | | TliI | Thermococcus litoralis | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, StrI, XhoI | | Tru1I | Thermus ruber RFL1 | TTAA | 1 | | | Tru9I | Thermus ruber 9 | TTAA | 1 | | | Tru201I | Thermus ruber 201 | RGATCY | 1 | | | TscI | Thermus sp. 491A | ACGT | 4 | | | TseI | Thermus sp. 93170 | GCWGC | 1 | AceI, ApeKI, SuiI, Taq52I | | Tsp1I | Thermus sp. 1 | ACTGG | 6 | | | Tsp32I | Thermus sp. 32 | TCGA | 1 | | | Tsp32II | Thermus sp. 32 | TCGA | 1 | | | Tsp45I | Thermus sp. YS45 | GTSAC | 1 | | | Tsp49I | Thermus sp. | ACGT | 4 | | | Tsp509I | Thermus sp. | AATT | 1 | | | TspBI | Thermophilic sp. | CCRYGG | 1 | | | Tsp4CI | Thermus sp. 4C | ACNGT | 3 | | | TspDTI | Thermus sp. DT | ATGAA | 10 | — None on May 2010 — | | TspEI | Thermus sp. 1E | AATT | 1 | | | TspGWI | Thermus sp. GW | ACGGA | 10 | | | TspMI = UthSI | Unidentified thermophile | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, SmaI, XcyI, XmaI, XmaCI | | TspRI | Thermus sp. R | CASTGNN | 7 | | | Tth111I | Thermus thermophilus 111 | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, TelI | | Tth111II | Thermus thermophilus 111 | CAARCA | 11 | | | TthHB8I | Thermus thermophilus HB8 | TCGA | 1 | | | Uba4009I | Unidentified bacterium A | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, RspLKII, SolI | | Uba153AI | Unidentified bacterium 153A | CAGCTG | 3 | | | UbaM39I | Unidentified bacterium M39 | CAGCTG | 3 | | | UnbI | Unidentified bacterium #8 | GGNCC | 1 | AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV, UnbI | | Uur960I | Ureaplasma urealyticum 960 | GCNGC | 2 | | | Vha464I | Vibrio harveyi 464 | CTTAAG | 1 | | | VneI | Vibrio nereis 18 | GTGCAC | 1 | Alw44I, ApaLI, SnoI | | VpaK32I | Vibrio parahaemolyticus 4387-61 | GCTCTTC | 8 | | | VpaK11AI | Vibrio parahaemolyticus 1743 | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11BI | | VpaK11BI | Vibrio parahaemolyticus 1743-1 | GGWCC | 1 | BsrAI, CauI, EagMI, FdiI, HgiBI, HgiJI, SinI, VpaK11AI | | VspI | Vibrio sp. 343 | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, Sru4DI | | XapI | Xanthomonas ampelina Slo 51-021 | RAATTY | 1 | AcsI, ApoI,  CfaI, FsiI | | XbaI | Xanthomonas badrii | TCTAGA | 1 | | | XcaI | Xanthomonas campestris | GTATAC | 3 | | | XceI | Xanthomonas campestris Ast 40-024 | RCATGY | 5 | | | XciI | Xanthomonas citri | GTCGAC | 1 | | | XcyI | Xanthomonas cyanopsidis 13D5 | CCCGGG | 1 | CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XmaI, XmaCI | | XhoI | Xanthomonas holcicola | CTCGAG | 1 | AbrI, BluI, BssHI, PanI, Sau3239I, Sfr274I, TliI, XpaI | | XhoII | Xanthomonas holcicola | RGATCY | 1 | | | XmaI | Xanthomonas malvacearum | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, TspMI, XcyI, XmaCI | | XmaIII | Xanthomonas malvacearum | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, SenPT16I | | XmaCI | Xanthomonas malvacearum C | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, Pac25I, PspAI, TspMI, XcyI, XmaI | | XmaJI | Xanthomonas maltophilia Jo 85-025 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, BspA2I | | XmiI | Xanthomonas maltophilia Jo 21-021 | GTMKAC | 2 | AccI, FblI | | XorII | Xanthomonas oryzae | CGATCG | 4 | Afa16RI, BspCI, EagBI, ErhB9I, MvrI, Ple19I, PvuI, RshI | | XpaI | Xanthomonas papavericola | CTCGAG | 1 | BssHI, MavI, PanI, SauLPII, Sbi68I, Sol10179I, StrI, XhoI | | XspI | Xanthomonas sp. YK1 | CTAG | 1 | | | YenI | Yersinia enterocolitica 08 A2635 | CTGCAG | 5 | Asp713I, BsuBI, CfrA4I, Ecl37kI, Psp23I, PstI, SalPI, SflI, Sst12I | | ZanI | Zymomonas anaerobia | CCWGG | 2 | ApaORI, BseBI, BspNI, BstNI, Bst2UI, CthII, EcoRII, MvaI, SspAI | | ZhoI | Zymomonas holcicola | ATCGAT | 2 | BanIII, BbvAII, BscI, BspJI, ClaI, LcaI, PgaI, SpmI, Ssp27144I | | ZraI | Zoogloea ramigera 11 | GACGTC | 3 | AatII, Ssp5230I | | ZrmI | Zoogloea ramigera SCA | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ScaI | | Zsp2I | Zoogloea sp. 2 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II |","Markdown" "Bioengineering","telatin/seqfu2","re/enzyme_table.md",".md","256435","1301","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:--------------|:----------------------------------------|:-----------------------|------:|:------------------------------------------------------------------------------------------------------| | Bac36I | Bacillus alcalophilus 36 | GGNCC | 1 | AspS9I, AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV | | BalI | Brevibacterium albidum | TGGCCA | 3 | | | Bal228I | Bacillus alcalophilus 228 | GGNCC | 1 | AspS9I, AvcI, BavAII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | | BamHI | Bacillus amyloliquefaciens H | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, Bce751I, Bsp98I, Bsp4009I, BspAAIII, CelI, Nsp29132II, NspSAIV, SolI, SurI | | BamNII | Bacillus amyloliquefaciens N | GGWCC | 1 | BcuAI, BsrAI, CauI, EagMI, FdiI, HgiCII, HgiJI, SinI | | BanI | Bacillus aneurinolyticus | GGYRCC | 1 | AccB1I, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BanII | Bacillus aneurinolyticus | GRGCYC | 5 | | | BanIII | Bacillus aneurinolyticus | ATCGAT | 2 | AagI, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | | BanAI | Bacillus anthracis | GGCC | 2 | | | BauI | Bacillus aquaemaris RFL1 | CACGAG | 1 | | | BavI | Bacillus alvei | CAGCTG | 3 | | | BavAI | Bacillus alvei A | CAGCTG | 3 | | | BavAII | Bacillus alvei A | GGNCC | 1 | AspS9I, AvcI, BavBII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | | BavBI | Bacillus alvei B | CAGCTG | 3 | | | BavBII | Bacillus alvei B | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, Bsu54I, FmuI, Pde12I | | BavCI | Bacillus alvei C | ATCGAT | 2 | AagI, BanIII, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | | BbeI | Bifidobacterium breve YIT4006 | GGCGCC | 5 | | | BbiII | Bifidobacterium bifidum YIT4007 | GRCGYC | 2 | AcyI, AhaII, BbiII, HgiHII, Hin1I, Hsp92I, Msp17I, PamII | | Bbi24I | Bifidobacterium bifidum S-24 | ACGCGT | 1 | | | BbrI | Bordetella bronchiseptica 4994 | AAGCTT | 1 | | | Bbr7I | Bacillus brevis 7 | GAAGAC | 9 | | | BbrPI | Bacillus brevis | CACGTG | 3 | AcvI, BcoAI, Eco72I, PmaCI, PmlI, PspCI | | BbsI | Bacillus laterosporus | GAAGAC | 8 | | | BbuI | Bacillus circulans | GCATGC | 5 | | | BbvI | Bacillus brevis | GCAGC | 8 | AlwXI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | | BbvII | Bacillus brevis 80 | GAAGAC | 8 | | | Bbv12I | Bacillus brevis 12 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | | Bbv16II | Bacillus brevis 16 | GAAGAC | 8 | | | BbvAII | Bacillus brevis A | ATCGAT | 2 | BavCI, Bci29I, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | | BbvAIII | Bacillus brevis A | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Bsu23I, Kpn2I | | BbvBI | Bacillus brevis B | GGYRCC | 1 | BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BbvCI | Bacillus brevis | CCTCAGC | 2 | AbeI | | Bca77I | Bacillus caldolyticus | WCCGGW | 1 | | | BccI | Bacteroides caccae | CCATC | 9 | | | Bce22I | Bacillus cereus 22 | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, FmuI, Pde12I | | Bce83I | Bacillus cereus 83 | CTTGAG | 12 | | | Bce243I | Bacillus cereus | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | | Bce751I | Bacillus cereus 751 | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, Bsp4009I, BstI, NspSAIV, Pfl8I | | BceAI | Bacillus cereus 1315 | ACGGC | 9 | | | BceBI | Bacillus cereus 1323 | CGCG | 2 | AccII, Bsh1236I, BtkI, Csp68KVI, FalII, FauBII, FnuDII, SelI, ThaI | | BcefI | Bacillus cereus fluorescens | ACGGC | 10 | | | Bci29I | Bacillus circulans 29 | ATCGAT | 2 | BavCI, BciBI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | | BciBI | Bacillus circulans B | ATCGAT | 2 | BavCI, BcmI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | | BciBII | Bacillus circulans B | CCWGG | 2 | AjnI, ApyI, BptI, Bst1I, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | | BciVI | Bacillus circulans | GTATCC | 10 | BfuI | | BclI | Bacillus caldolyticus | TGATCA | 1 | AbaI, BsiQI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | | BcmI | Bacillus sp. | ATCGAT | 2 | BsuTUI, Bsu15I, BavCI, Bli86I, BspZEI, Rme21I, BseCI, BdiI | | BcnI | Bacillus centrosporus RFL1 | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, Eco1831I, HgiS22I,Kpn49kII, NciI | | BcoI | Bacillus coagulans SM 1 | CYCGRG | 1 | Ama87I, AquI, BsoBI, BstSI, Eco88I, NspSAI, OfoI, PunAI | | Bco5I | Bacillus coagulans 5 | CTCTTC | 7 | | | Bco27I | Bacillus coagulans 27 | CCGG | 1 | | | Bco116I | Bacillus coagulans 116 | CTCTTC | 7 | | | Bco118I | Bacillus coagulans 118 | RCCGGY | 1 | | | BcoAI | Bacillus coagulans AUCM B-732 | CACGTG | 3 | AcvI, BbrPI, Eco72I, PmaCI, PmlI, PspCI | | BcoKI | Bacillus coagulans | CTCTTC | 7 | | | BcuI | Bacillus coagulans Vs 29-022 | ACTAGT | 1 | AhII, AclNI, SpeI | | BcuAI | Bacillus cereus BKM B-814 | GGWCC | 1 | BamNxI, BsrAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI | | BdiI | Brevibacterium divaricatum | ATCGAT | 2 | BavCI, Bci29I, Bli41I, Bli86I, BseCI, BsuTUI, Rme21I, SpmI | | BdiSI | Bacteroides distasonis | CTRYAG | 1 | | | BecAII | Brevibacterium sp. A | GGCC | 2 | | | BepI | Brevibacterium epidermidis | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, BtkI, FalII, FauBII, ThaI | | BetI | Brevibacterium acetyliticum | WCCGGW | 1 | | | BfaI | Bacteroides fragilis | CTAG | 1 | | | BfiI | Bacillus firmus S8120 | ACTGGG | 11 | BmrI | | Bfi57I | Butyrivibrio fibrisolvens OB157 | GATC | 1 | Bsp105I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, SsiBI | | Bfi89I | Butyrivibrio fibrisolvens OB189 | YGGCCR | 1 | | | BfmI | Bacillus firmus S8-336 | CTRYAG | 1 | | | BfrI | Bacteroides fragilis | CTTAAG | 1 | | | BfrBI | Bacteroides fragilis BE3 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | | BfuI | Bacillus firmus Auk 22-m21 | GTATCC | 10 | BciVI | | BfuAI | Bacillus fusiformis | ACCTGC | 10 | Acc36I, BspMI, BveI | | BfuCI | Bacillus fusiformis 1226 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, MkrAI, Sth368I | | BglII | Bacillus globigii | AGATCT | 1 | | | BimI | Brevibacterium immotum | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | | Bim19I | Brevibacterium immotum 19 | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | | Bim19II | Brevibacterium immotum 19 | GGCC | 2 | | | BinI | Bifidobacterium infantis 659 | GGATC | 9 | AclWI, AlwI,  BsrWI, BspPI, BstH9I,  Bth617I, EacI | | BlfI | Bacillus licheniformis | TCCGGA | 1 | AccIII, Aor13HI, BseAI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | | Bli41I | Bacillus licheniformis 41 | ATCGAT | 2 | Bci29I, Bli86I, BseCI, BsiXI, BsuTUI, Rme21I, SpmI, Ssp27144I | | Bli86I | Bacillus licheniformis 86 | ATCGAT | 2 | BliAI, Bli41I, BseDI, BsiXI, Rme21I, SpmI, Ssp27144I, ZhoI | | Bli736I | Bacillus licheniformis 736 | GGTCTC | 7 | | | BliAI | Bacillus licheniformis | ATCGAT | 2 | BliRI, Bli41I, BsiXI, BspDI, Rme21I, SpmI, Ssp27144I, ZhoI | | BliHKI | Bacillus licheniformis HK | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | | BliRI | Bacillus licheniformis | ATCGAT | 2 | BciBI, BdiI, Bli41I, BsiXI, BspDI, BspXI, LplI, SpmI, ZhoI | | BlnI | Brevibacterium linens | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BspA2I, XmaJI | | BloHI | Bifidobacterium longum E194b | RGATCY | 1 | | | BloHII | Bifidobacterium longum E194b | CTGCAG | 5 | AjoI, Asp713I, BsuBI, CflI, CfuII, HalII, PstI, SalPI, SflI, Sst12I | | BlpI | Bacillus lentus | GCTNAGC | 2 | | | BluI | Brevibacterium luteum | CTCGAG | 1 | AbrI, BssHI, BstVI, PanI, Sau3239I, Sfr274I, TliI, XhoI | | Bme12I | Bacillus megaterium 12 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, SsiBI | | Bme18I | Bacillus megaterium 18 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI | | Bme142I | Bacillus megaterium 142 | RGCGCY | 3 | AccB2I,  BfoI, Bsp143II, BstH2I, HaeII, LpnI | | Bme216I | Bacillus megaterium 216 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | | Bme361I | Bacillus megaterium 361 | GGCC | 2 | | | Bme585I | Bacillus mesentericus 585 | CCCGC | 9 | | | Bme1390I | Bacillus megaterium RFL1390 | CCNGG | 2 | | | Bme1580I | Bacillus megaterium 1580 | GKGCMC | 5 | | | BmgBI | Bacillus megaterium | CACGTC | 3 | | | BmrI | Bacillus megaterium | ACTGGG | 11 | BfiI | | BmtI | Bacillus megaterium S2 | GCTAGC | 5 | AceII, AsuNHI,  BspOI, NheI, LlaG2I, PstNHI | | BmyI | Bacillus mycoides | GDGCHC | 5 | AocII, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | | BnaI | Bacillus natto B3364 | GGATCC | 1 | AccEBI, BamHI, Bce751I, BstI, CelI, OkrAI, Nsp29132II, Pfl8I, SolI | | BpcI | Bacillus sphaericus | CTRYAG | 1 | | | BpiI | Bacillus pumilus sw 4-3 | GAAGAC | 8 | | | BpmI | Bacillus pumilus | CTGGAG | 12 | | | BpoAI | Bacillus polymyxa | ATTAAT | 2 | AseI, AsnI, PshBI, Sru4DI, VspI | | BptI | Bacillus pantothenticus | CCWGG | 2 | AjnI, BseBI, Bse16I, BstNI, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | | BpuI | Bacillus pumilus AHU1387A | GRGCYC | 5 | | | Bpu10I | Bacillus pumilus 10 | CCTNAGC | 2 | | | Bpu14I | Bacillus pumilus 14 | TTCGAA | 2 | AcpI, AsuII, BsiCI, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | | Bpu95I | Bacillus pumilus 95 | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | | Bpu1102I | Bacillus pumilus RFL1102 | GCTNAGC | 2 | | | BpuAI | Bacillus pumilus | GAAGAC | 8 | | | BpuAmI | Bacillus pumilus | GAGCTC | 3 | | | BpuB5I | Bacillus pumilus | CGTACG | 1 | | | BpuDI | Bacillus pumilus 1117 | CCTNAGC | 2 | | | BpuEI | Bacillus pumilus 2187a | CTTGAG | 12 | | | BpuJI | Bacillus pumilus RFL1458 | CCCGT | 9 | — None on May 2010 — | | BpuSI | Bacillus pumilus | GGGAC | 8 | | | BsaI | Bacillus stearothermophilus 20241 | GGTCTC | 7 | Bso31I, BspTNI, Eco31I | | Bsa29I | Bacillus sp. 29 | ATCGAT | 2 | AagI, BanIII, BavCI, BseCI, BspDI, Bsu15I, BsuTUI, ClaI, BbvAII | | BsaAI | Bacillus stearothermophilus G668 | YACGTR | 3 | | | BsaHI | Bacillus stearothermophilus CPW11 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BbiII, BstACI, HgiI, PamII | | BsaJI | Bacillus stearothermophilus J695 | CCNNGG | 1 | | | BsaMI | Bacillus stearothermophilus M293 | GAATGC | 7 | Asp26HI, Asp35HI, Asp36HI, Asp50HI, BsaMI, BsmI, Mva1269I | | BsaOI | Bacillus stearothermophilus O-122 | CGRYCG | 4 | | | BsaWI | Bacillus stearothermophilus W1718 | WCCGGW | 1 | | | BscI | Bacillus sp. | ATCGAT | 2 | BanIII, BavCI, Bci29I, BdiI, Bli41I, BliAI, LplI, PgaI, SpmI | | Bsc91I | Bacillus sp. | GAAGAC | 8 | | | BscAI | Bacillus schlegelii S3 | GCATC | 9 | | | BscBI | Bacillus sp. A11 | GGNNCC | 3 | AspNI,  BmiI, BspLI, NlaIV, PspN4I | | BscCI | Bacillus sp. 2G | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI, Asp36HI, BsaMI, BscCI, PctI | | BscFI | Bacillus sp. JY391 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, CviAI, Kzo9I, NlaII, SsiBI | | Bse1I | Bacillus stearothermophilus 1 | ACTGG | 6 | | | Bse15I | Bacillus sp. 15 | CYCGRG | 1 | Ama87I, AvaI, BcoI, BsoBI, BstSI, Eco88I, NspSAI, OfoI | | Bse16I | Bacillus sp. 16 | CCWGG | 2 | AeuI, BseBI, BsiLI, BstNI, BstM6I, BthDI, BthEI, EcoRII, MvaI | | Bse17I | Bacillus sp. 17 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | | Bse21I | Bacillus sp. 21 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | | Bse24I | Bacillus sp. 24 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | | Bse64I | Bacillus sp. 64 | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BstPI, EcaI, Eci125I, EcoO65I, NspSAII | | Bse118I | Bacillus sp. 118 | RCCGGY | 1 | | | Bse634I | Bacillus sp. 634 | RCCGGY | 1 | | | BseAI | Bacillus sphaericus | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, Kpn2I | | BseBI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, AorI, Bse17I, Bst1I, BstOI, Bst2UI, EcoRII, MvaI, SleI, ZanI | | BseCI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BspDI, Bsu15I, BsuTUI, ClaI, LcaI | | BseDI | Bacillus stearothermophilus RFL1434 | CCNNGG | 1 | | | Bse3DI | Bacillus stearothermophilus 3D | GCAATG | 8 | | | BseGI | Bacillus stearothermophilus Vs 34-031 | GGATG | 7 | | | BseKI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | | BseMI | Bacillus stearothermophilus Isl 15-111 | GCAATG | 8 | | | BseMII | Bacillus stearothermophilus Isl 15-111 | CTCAG | 10 | | | BseNI | Bacillus sp. N | ACTGG | 6 | | | BsePI | Bacillus stearothermophilus P6 | GCGCGC | 1 | | | BseQI | Bacillus sp. Q | GGCC | 2 | | | BseRI | Bacillus sp. R | GAGGAG | 11 | | | BseSI | Bacillus stearothermophilus Jo-553 | GKGCMC | 5 | | | BseT9I | Bacillus sp. T9 | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstT9I, EcaI, Eci125I, EcoO65I, NspSAII, PspEI | | BseT10I | Bacillus sp. T10 | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT10I, BstPI, EcoO128I, EcoO65I, PspEI | | BseXI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseKI, Bsp423I, Bst12I, Bst71I, BstV1I | | BseX3I | Bacillus stearothermophilus X3 | CGGCCG | 1 | AaaI, BstZI, EagI, EclXI, Eco52I, SenPT16I, XmaIII | | BseYI | Bacillus sp. 2521 | CCCAGC | 1 | | | BseZI | Bacillus sp. Z | CTCTTC | 7 | | | BsgI | Bacillus sphaericus B922 | GTGCAG | 13 | | | BshI | Bacillus sphaericus | GGCC | 2 | | | Bsh45I | Bacillus sphaericus 45 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | | Bsh1236I | Bacillus sphaericus RFL1236 | CGCG | 2 | AccII, BceBI, BspFNI, Bsp50I, Csp68KVI, FauBII, MvnI, SelI | | Bsh1285I | Bacillus sphaericus RFL1285 | CGRYCG | 4 | | | BshFI | Bacillus sphaericus | GGCC | 2 | | | BshGI | Bacillus sphaericus | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, PspGI, SspAI | | BshKI | Bacillus sphaericus | GGNCC | 1 | AspS9I, Bac36I, BavAII, Bsp1894I, BspBII, CcuI, MaeK81II, Pde12I | | BshNI | Bacillus sphaericus TK-45 | GGYRCC | 1 | BanI, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BshTI | Bacillus sphaericus Jo22-024 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, CsiAI CspAI, PinAI | | BsiI | Bacillus sphaericus | CACGAG | 1 | | | BsiCI | Bacillus sp. | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, Csp45I, FspII, NspV, PpaAI, SfuI | | BsiEI | Bacillus sp. | CGRYCG | 4 | | | BsiHKAI | Bacillus stearothermophilus | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I,  Bsm6I, HgiAI, MspV281I | | BsiHKCI | Bacillus sp. HKC | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | | BsiKI | Bacillus sp. | GGTNACC | 1 | | | BsiLI | Bacillus sp. | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, BstNI, Bst38I, Bst100I, EcoRII, MvaI | | BsiMI | Bacillus sp. | TCCGGA | 1 | AccIII, BbvAIII, BlfI, Bsp13I, BspMII, Bsu23I, Kpn2I, PinBII | | BsiQI | Bacillus sp. | TGATCA | 1 | AbaI, BclI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | | BsiSI | Bacillus sp. | CCGG | 1 | | | BsiWI | Bacillus sp. | CGTACG | 1 | | | BsiXI | Bacillus sp. X | ATCGAT | 2 | BscI, BsiXI, Bsp106I, BspDI, Bsu15I, BsuTUI, ClaI, Rme21I | | BsiZI | Bacillus sp. | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | | BslFI | Bacillus stearothermophilus FI | GGGAC | 9 | | | BsmI | Bacillus stearothermophilus NUB | GAATGC | 7 | Asp26HI, Asp36HI, Asp40HI, BmaHI, BscCI, Mva1269I, PctI | | BsmAI | Bacillus stearothermophilus A664 | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsoMAI, BstMAI | | BsmBI | Bacillus stearothermophilus B61 | CGTCTC | 7 | | | BsmFI | Bacillus stearothermophilus F | GGGAC | 9 | | | BsmSI | Bacillus stearothermophilus CP114 | CCWWGG | 1 | | | Bso31I | Bacillus stearothermophilus E31 | GGTCTC | 7 | | | BsoBI | Bacillus stearothermophilus JN2091 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | | BsoCI | Bacillus stearothermophilus AU891 | GDGCHC | 5 | AocII, BmyI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | | BsoFI | Bacillus stearothermophilus F66 | GCNGC | 2 | | | BsoMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BstMAI | | Bsp6I | Bacillus sp. RFL6 | GCNGC | 2 | | | Bsp13I | Bacillus sp. 13 | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | | Bsp19I | Bacillus sp. 19 | CCATGG | 1 | | | Bsp50I | Bacillus sp. RFL50 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | | Bsp63I | Bacillus sphaericus 63 | CTGCAG | 5 | AjoI, Asp713I, BloHII, MhaAI, Pfl21I, PstI, SalPI, SflI, Sst12I, YenI | | Bsp67I | Bacillus sphaericus 67 | GATC | 1 | AspMDI, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp68I | Bacillus sp. RFL68 | TCGCGA | 3 | NruI | | Bsp98I | Bacillus sp. RFL98 | GGATCC | 1 | AccEBI, AliI, BamHI, BnaI, BstI, CelI, OkrAI, NspSAIV, Pfl8I, SurI | | Bsp105I | Bacillus sphaericus 105 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp106I | Bacillus sphaericus 106 | ATCGAT | 2 | BbvAII, Bci29I, BciBI, BcmI, BspOVII, BstNZ169I, Rme21I | | Bsp119I | Bacillus sp. RFL119 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, FspII, NspV, SspRFI | | Bsp120I | Bacillus sp. RFL120 | GGGCCC | 1 | ApaI, PpeI, PspOMI | | Bsp123I | Bacillus sp. 123 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | | Bsp143I | Bacillus sp. RFL143 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I, Sau3AI | | Bsp143II | Bacillus sp. RFL143 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, BstH2I, HaeII, LpnI | | Bsp211I | Bacillus sphaericus 211 | GGCC | 2 | | | Bsp423I | Bacillus sp. 423 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bst12I, Bst71I, BstV1I | | Bsp519I | Bacillus sp. 519 | GRGCYC | 5 | | | Bsp1286I | Bacillus sphaericus | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, NspII, SduI | | Bsp1407I | Bacillus stearothermophilus RFL1407 | TGTACA | 1 | AauI,  BsmRI, BsrGI, BstAUI, Ssp4800I, SspBI | | Bsp1720I | Bacillus sp. 1720 | GCTNAGC | 2 | | | Bsp1894I | Bacillus sphaericus 1894 | GGNCC | 1 | AspS9I, Bac36I, BavBII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | | Bsp2095I | Bacillus sphaericus 2095 | GATC | 1 | Bfi57I, Bsp143I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp4009I | Bacillus sp. 4009 | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, BstI, CelI, OkrAI, Pfl8I, RspLKII, SurI | | BspAI | Bacillus sphaericus JL4B | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | BspA2I | Bacillus sp. A2 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, XmaJI | | Bsp153AI | Bacillus sp. 153A | CAGCTG | 3 | | | BspAAI | Bacillus sp. AA | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | | BspAAII | Bacillus sp. AA | TCTAGA | 1 | | | BspAAIII | Bacillus sp. AA | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, Pfl8I, RspLKII, SolI | | BspANI | Bacillus sp. AN | GGCC | 2 | | | BspBI | Bacillus sphaericus JL14 | CTGCAG | 5 | AjoI, ApiI, Asp713I, BloHII, CfrA4I, Pfl21I, PstI, SalPI, Sst12I, YenI | | BspBII | Bacillus sphaericus JL14 | GGNCC | 1 | AsuI, Bac36I, BavBII, BshKI, BspF4I, CcuI, MaeK81II, PspPI | | BspBRI | Bacillus sp. | GGCC | 2 | | | BspBS31I | Bacillus sp. BS31 | GAAGAC | 8 | | | BspCI | Bacillus sp. C1 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, ErhB9I, NblI, Psu161I, RshI, XorII | | BspCNI | Bacillus sp. 1310 | CTCAG | 10 | | | BspDI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, Bsu15I, BsuTUI, ClaI, ZhoI | | BspD6I | Bacillus sp. D6 | GACTC | 9 | | | BspEI | Bacillus sp. | TCCGGA | 1 | AccIII, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, MroI, PinBII | | BspFI | Bacillus sp. | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | BspF4I | Bacillus sp. F4 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | | BspHI | Bacillus sp. H3 | TCATGA | 1 | | | BspIS4I | Bacillus sp. IS4 | GAAGAC | 8 | | | BspJI | Bacillus sp. | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NmeCI, SsiAI | | BspJII | Bacillus sp. | ATCGAT | 2 | Bsa29I, BseCI, Bsp106I, BspDI, BspOVII, BspXI, BspZEI | | BspKI | Bacillus sp. K | GGCC | 2 | | | BspKT5I | Bacillus sp. | CTGAAG | 13 | | | BspKT6I | Bacillus sp. KT6 | GATC | 3 | BfuCI, Bsp2095I, Bst19II, BstKTI, DpnII, LlaAI, NmeCI, SsiAI | | BspKT8I | Bacillus sp. KT8 | AAGCTT | 1 | | | BspLI | Bacillus sp. RJ3-212 | GGNNCC | 3 | AspNI, BscBI,  BmiI, NlaIV, PspN4I | | BspLAI | Bacillus sp. LA | GCGC | 3 | AspLEI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | | BspLAII | Bacillus sp. LA | TTCGAA | 2 | | | BspLAIII | Bacillus sp. LA | AAGCTT | 1 | | | BspLS2I | Bacillus sp. LS2 | GDGCHC | 5 | AocII, BmyI, BsoCI, BspLS2I, MhlI, NspII, SduI | | BspLU4I | Bacillus sp. LU4 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, NspSAI, OfoI | | BspLU11I | Bacillus sp. LU11 | ACATGT | 1 | | | BspLU11III | Bacillus sp. LU11 | GGGAC | 9 | | | BspMI | Bacillus sp. M | ACCTGC | 10 | Acc36I, BfuAI, BveI | | BspMII | Bacillus sp. M | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspEI, Bsu23I, CauB3I, MroI | | BspM39I | Bacillus sp. M39 | CAGCTG | 3 | | | BspM90I | Bacillus sp. M90 | GTATAC | 3 | | | BspMAI | Bacillus stearothermophilus MA | CTGCAG | 5 | AjoI, Asp713I, BloHII, PaePI, Psp23I, PstI, SalPI, Sst12I, YenI | | BspMKI | Bacillus sp. MKI | GTCGAC | 1 | | | BspNI | Bacillus sp. N | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | | BspO4I | Bacillus sp. O-4 | CAGCTG | 3 | | | BspOVII | Bacillus sp. OV | ATCGAT | 2 | BanIII, BavCI, BciBI, BcmI, Bli86I, BliRI, BspJII, BstNZ169I, SpmI | | BspPI | Bacillus sp. d 1-34 | GGATC | 9 | AclWI, AlwI, BinI,  BsrWI, BstH9I,  Bst31TI, Bth617I, EacI | | BspRI | Bacillus sphaericus R | GGCC | 2 | | | BspR7I | Bacillus sp. R7 | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | | BspST5I | Bacillus sp. ST5 | GCATC | 8 | | | BspTI | Bacillus sp. RFL1265 | CTTAAG | 1 | AflII | | BspT104I | Bacillus sp. T104 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BstBI, Csp45I, LspI, NspV, SspRFI | | BspT107I | Bacillus sp. T107 | GGYRCC | 1 | AccB1I, BanI, BbvBI, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BspTNI | Bacillus sp. TN | GGTCTC | 7 | | | BspTS514I | Bacillus sp. TS514 | GAAGAC | 8 | | | BspXI | Bacillus sphaericus X | ATCGAT | 2 | BliAI, BliRI, BscI, Bst28I, Bsu15I, LcaI, PgaI, Ssp27144I, ZhoI | | BspXII | Bacillus sphaericus X | TGATCA | 1 | AbaI, BclI, BsiQI, BstT7I, FbaI, Ksp22I,  ParI | | BspZEI | Bacillus sp. ZE | ATCGAT | 2 | Bsa29I, BseCI, BspDI, BspXI, Bst28I, BstNZ169I, BsuTUI, LplI | | BsrI | Bacillus stearothermophilus | ACTGG | 6 | | | BsrAI | Bacillus stearothermophilus CPW7 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | | BsrBI | Bacillus stearothermophilus CPW193 | CCGCTC | 3 | AccBSI, BstD102I, Bst31NI, MbiI | | BsrDI | Bacillus stearothermophilus D70 | GCAATG | 8 | | | BsrFI | Bacillus stearothermophilus CPW16 | RCCGGY | 1 | | | BsrGI | Bacillus stearothermophilus GR75 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BstAUI, Ssp4800I, SspBI | | BsrSI | Bacillus stearothermophilus CPW19 | ACTGG | 6 | | | BssAI | Bacillus sp. | RCCGGY | 1 | | | BssECI | Bacillus stearothermophilus EC | CCNNGG | 1 | | | BssHI | Bacillus stearothermophilus H3 | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | | BssHII | Bacillus stearothermophilus H3 | GCGCGC | 1 | | | BssIMI | Bacillus stearothermophilus IM | GGGTC | 2 | | | BssKI | Bacillus stearothermophilus TBI | CCNGG | 1 | | | BssNAI | Bacillus stearothermophilus NA | GTATAC | 3 | | | BssNI | Bacillus sphaericus KTN | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, Hsp92I, Msp17I | | BssSI | Bacillus stearothermophilus S719 | CACGAG | 1 | | | BssT1I | Bacillus stearothermophilus T1 | CCWWGG | 1 | | | Bsp6I | Bacillus sp. RFL6 | GCNGC | 2 | | | Bsp13I | Bacillus sp. 13 | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | | Bsp19I | Bacillus sp. 19 | CCATGG | 1 | | | Bsp50I | Bacillus sp. RFL50 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | | Bsp63I | Bacillus sphaericus 63 | CTGCAG | 5 | AjoI, Asp713I, BloHII, MhaAI, Pfl21I, PstI, SalPI, SflI, Sst12I, YenI | | Bsp67I | Bacillus sphaericus 67 | GATC | 1 | AspMDI, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp68I | Bacillus sp. RFL68 | TCGCGA | 3 | NruI | | Bsp98I | Bacillus sp. RFL98 | GGATCC | 1 | AccEBI, AliI, BamHI, BnaI, BstI, CelI, OkrAI, NspSAIV, Pfl8I, SurI | | Bsp105I | Bacillus sphaericus 105 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp106I | Bacillus sphaericus 106 | ATCGAT | 2 | BbvAII, Bci29I, BciBI, BcmI, BspOVII, BstNZ169I, Rme21I | | Bsp119I | Bacillus sp. RFL119 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, FspII, NspV, SspRFI | | Bsp120I | Bacillus sp. RFL120 | GGGCCC | 1 | ApaI, PpeI, PspOMI | | Bsp123I | Bacillus sp. 123 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | | Bsp143I | Bacillus sp. RFL143 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I, Sau3AI | | Bsp143II | Bacillus sp. RFL143 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, BstH2I, HaeII, LpnI | | Bsp211I | Bacillus sphaericus 211 | GGCC | 2 | | | Bsp423I | Bacillus sp. 423 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bst12I, Bst71I, BstV1I | | Bsp519I | Bacillus sp. 519 | GRGCYC | 5 | | | Bsp1286I | Bacillus sphaericus | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, NspII, SduI | | Bsp1407I | Bacillus stearothermophilus RFL1407 | TGTACA | 1 | AauI,  BsmRI, BsrGI, BstAUI, Ssp4800I, SspBI | | Bsp1720I | Bacillus sp. 1720 | GCTNAGC | 2 | | | Bsp1894I | Bacillus sphaericus 1894 | GGNCC | 1 | AspS9I, Bac36I, BavBII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | | Bsp2095I | Bacillus sphaericus 2095 | GATC | 1 | Bfi57I, Bsp143I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp4009I | Bacillus sp. 4009 | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, BstI, CelI, OkrAI, Pfl8I, RspLKII, SurI | | BspAI | Bacillus sphaericus JL4B | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | BspA2I | Bacillus sp. A2 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, XmaJI | | Bsp153AI | Bacillus sp. 153A | CAGCTG | 3 | | | BspAAI | Bacillus sp. AA | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | | BspAAII | Bacillus sp. AA | TCTAGA | 1 | | | BspAAIII | Bacillus sp. AA | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, Pfl8I, RspLKII, SolI | | BspANI | Bacillus sp. AN | GGCC | 2 | | | BspBI | Bacillus sphaericus JL14 | CTGCAG | 5 | AjoI, ApiI, Asp713I, BloHII, CfrA4I, Pfl21I, PstI, SalPI, Sst12I, YenI | | BspBII | Bacillus sphaericus JL14 | GGNCC | 1 | AsuI, Bac36I, BavBII, BshKI, BspF4I, CcuI, MaeK81II, PspPI | | BspBRI | Bacillus sp. | GGCC | 2 | | | BspBS31I | Bacillus sp. BS31 | GAAGAC | 8 | | | BspCI | Bacillus sp. C1 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, ErhB9I, NblI, Psu161I, RshI, XorII | | BspCNI | Bacillus sp. 1310 | CTCAG | 10 | | | BspDI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, Bsu15I, BsuTUI, ClaI, ZhoI | | BspD6I | Bacillus sp. D6 | GACTC | 9 | | | BspEI | Bacillus sp. | TCCGGA | 1 | AccIII, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, MroI, PinBII | | BspFI | Bacillus sp. | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | BspF4I | Bacillus sp. F4 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | | BspHI | Bacillus sp. H3 | TCATGA | 1 | | | BspIS4I | Bacillus sp. IS4 | GAAGAC | 8 | | | BspJI | Bacillus sp. | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NmeCI, SsiAI | | BspJII | Bacillus sp. | ATCGAT | 2 | Bsa29I, BseCI, Bsp106I, BspDI, BspOVII, BspXI, BspZEI | | BspKI | Bacillus sp. K | GGCC | 2 | | | BspKT5I | Bacillus sp. | CTGAAG | 13 | | | BspKT6I | Bacillus sp. KT6 | GATC | 3 | BfuCI, Bsp2095I, Bst19II, BstKTI, DpnII, LlaAI, NmeCI, SsiAI | | BspKT8I | Bacillus sp. KT8 | AAGCTT | 1 | | | BspLI | Bacillus sp. RJ3-212 | GGNNCC | 3 | AspNI, BscBI,  BmiI, NlaIV, PspN4I | | BspLAI | Bacillus sp. LA | GCGC | 3 | AspLEI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | | BspLAII | Bacillus sp. LA | TTCGAA | 2 | | | BspLAIII | Bacillus sp. LA | AAGCTT | 1 | | | BspLS2I | Bacillus sp. LS2 | GDGCHC | 5 | AocII, BmyI, BsoCI, BspLS2I, MhlI, NspII, SduI | | BspLU4I | Bacillus sp. LU4 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, NspSAI, OfoI | | BspLU11I | Bacillus sp. LU11 | ACATGT | 1 | | | BspLU11III | Bacillus sp. LU11 | GGGAC | 9 | | | BspMI | Bacillus sp. M | ACCTGC | 10 | Acc36I, BfuAI, BveI | | BspMII | Bacillus sp. M | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspEI, Bsu23I, CauB3I, MroI | | BspM39I | Bacillus sp. M39 | CAGCTG | 3 | | | BspM90I | Bacillus sp. M90 | GTATAC | 3 | | | BspMAI | Bacillus stearothermophilus MA | CTGCAG | 5 | AjoI, Asp713I, BloHII, PaePI, Psp23I, PstI, SalPI, Sst12I, YenI | | BspMKI | Bacillus sp. MKI | GTCGAC | 1 | | | BspNI | Bacillus sp. N | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | | BspO4I | Bacillus sp. O-4 | CAGCTG | 3 | | | BspOVII | Bacillus sp. OV | ATCGAT | 2 | BanIII, BavCI, BciBI, BcmI, Bli86I, BliRI, BspJII, BstNZ169I, SpmI | | BspPI | Bacillus sp. d 1-34 | GGATC | 9 | AclWI, AlwI, BinI,  BsrWI, BstH9I,  Bst31TI, Bth617I, EacI | | BspRI | Bacillus sphaericus R | GGCC | 2 | | | BspR7I | Bacillus sp. R7 | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | | BspST5I | Bacillus sp. ST5 | GCATC | 8 | | | BspTI | Bacillus sp. RFL1265 | CTTAAG | 1 | AflII | | BspT104I | Bacillus sp. T104 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BstBI, Csp45I, LspI, NspV, SspRFI | | BspT107I | Bacillus sp. T107 | GGYRCC | 1 | AccB1I, BanI, BbvBI, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BspTNI | Bacillus sp. TN | GGTCTC | 7 | | | BspTS514I | Bacillus sp. TS514 | GAAGAC | 8 | | | BspXI | Bacillus sphaericus X | ATCGAT | 2 | BliAI, BliRI, BscI, Bst28I, Bsu15I, LcaI, PgaI, Ssp27144I, ZhoI | | BspXII | Bacillus sphaericus X | TGATCA | 1 | AbaI, BclI, BsiQI, BstT7I, FbaI, Ksp22I,  ParI | | BspZEI | Bacillus sp. ZE | ATCGAT | 2 | Bsa29I, BseCI, BspDI, BspXI, Bst28I, BstNZ169I, BsuTUI, LplI | | BsrI | Bacillus stearothermophilus | ACTGG | 6 | | | BsrAI | Bacillus stearothermophilus CPW7 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | | BsrBI | Bacillus stearothermophilus CPW193 | CCGCTC | 3 | AccBSI, BstD102I, Bst31NI, MbiI | | BsrDI | Bacillus stearothermophilus D70 | GCAATG | 8 | | | BsrFI | Bacillus stearothermophilus CPW16 | RCCGGY | 1 | | | BsrGI | Bacillus stearothermophilus GR75 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BstAUI, Ssp4800I, SspBI | | BsrSI | Bacillus stearothermophilus CPW19 | ACTGG | 6 | | | BssAI | Bacillus sp. | RCCGGY | 1 | | | BssECI | Bacillus stearothermophilus EC | CCNNGG | 1 | | | BssHI | Bacillus stearothermophilus H3 | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | | BssHII | Bacillus stearothermophilus H3 | GCGCGC | 1 | | | BssIMI | Bacillus stearothermophilus IM | GGGTC | 2 | | | BssKI | Bacillus stearothermophilus TBI | CCNGG | 1 | | | BssNAI | Bacillus stearothermophilus NA | GTATAC | 3 | | | BssNI | Bacillus sphaericus KTN | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, Hsp92I, Msp17I | | BssSI | Bacillus stearothermophilus S719 | CACGAG | 1 | | | BssT1I | Bacillus stearothermophilus T1 | CCWWGG | 1 | | | BstI | Bacillus stearothermophilus 1503-4R | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, Nsp29132II | | Bst1I | Bacillus stearothermophilus 1 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | | Bst2I | Bacillus stearothermophilus 2 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, BstOI, Bst2UI, CthII, EcoRII, MvaI | | Bst6I | Bacillus stearothermophilus 6 | CTCTTC | 7 | | | Bst11I | Bacillus stearothermophilus 11 | ACTGG | 6 | | | Bst12I | Bacillus stearothermophilus 12 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst71I, BstV1I | | Bst19I | Bacillus stearothermophilus 19 | GCATC | 9 | | | Bst19II | Bacillus stearothermophilus 19 | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | | Bst28I | Bacillus stearothermophilus 28 | ATCGAT | 2 | BciBI, BdiI, Bli41I, Bsa29I, Bsp106I, BspDI, LplI, SpmI, ZhoI | | Bst38I | Bacillus stearothermophilus 38 | CCWGG | 2 | AorI, BseBI, Bse17I, BsiLI, BspNI, BstOI, Bst2UI, EcoRII, MvaI | | Bst40I | Bacillus stearothermophilus 40 | CCGG | 1 | | | Bst71I | Bacillus stearothermophilus 71 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, BstV1I | | Bst98I | Bacillus stearothermophilus C98 | CTTAAG | 1 | | | Bst100I | Bacillus stearothermophilus 100 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | | Bst1107I | Bacillus stearothermophilus RFL1107 | GTATAC | 3 | | | BstACI | Bacillus stearothermophilus AC | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, HgiDI, Hsp92I | | BstAUI | Bacillus stearothermophilus AU | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, Ssp4800I, SspBI | | BstBI | Bacillus stearothermophilus B225 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, LspI, NspV, SspRFI | | Bst2BI | Bacillus stearothermophilus 2B | CACGAG | 1 | | | BstBAI | Bacillus stearothermophilus BA | YACGTR | 3 | | | BstBSI | Bacillus stearothermophilus BS | GTATAC | 3 | | | BstB7SI | Bacillus stearothermophilus B7S | RCCGGY | 1 | | | BstBS32I | Bacillus stearothermophilus BS32 | GAAGAC | 8 | | | BstBZ153I | Bacillus stearothermophilus BZ153 | GCGCGC | 1 | | | Bst4CI | Bacillus stearothermophilus 4C | ACNGT | 3 | | | BstC8I | Bacillus stearothermophilus C8 | GCNNGC | 3 | | | BstD102I | Bacillus stearothermophilus D102 | CCGCTC | 3 | AccBSI, BsrBI, Bst31NI, MbiI | | BstDEI | Bacillus stearothermophilus DE | CTNAG | 1 | | | BstDSI | Bacillus stearothermophilus DS | CCRYGG | 1 | | | BstEII | Bacillus stearothermophilus ET | GGTNACC | 1 | AcrII, BstPI, BstT9I, BstT10I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | | BstENII | Bacillus stearothermophilus EN | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | | BstEZ359I | Bacillus stearothermophilus EZ359 | GTTAAC | 3 | | | BstFI | Bacillus stearothermophilus FH58 | AAGCTT | 1 | | | BstF5I | Bacillus stearothermophilus F5 | GGATG | 7 | | | BstFNI | Bacillus stearothermophilus | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BstUI, Csp68KVI, FauBII, MvnI, SelI | | BstFZ438I | Bacillus stearothermophilus FZ438 | CCCGC | 9 | | | BstGZ53I | Bacillus stearothermophilus GZ53 | CGTCTC | 7 | | | BstH2I | Bacillus stearothermophilus H2 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, HaeII, LpnI | | BstH9I | Bacillus stearothermophilus H9 | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI,  Bst31TI, BthII, Bth617I, EacI | | BstHHI | Bacillus stearothermophilus HH | GCGC | 3 | AspLEI, BspLAI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | | BstHPI | Bacillus stearothermophilus HP | GTTAAC | 3 | | | BstIZ316I | Bacillus stearothermophilus IZ316 | CACNNNGTG | 6 | AdeI, DraIII | | BstJZ301I | Bacillus stearothermophilus JZ301 | CTNAG | 1 | | | BstKTI | Bacillus stearothermophilus KT | GATC | 3 | AspMDI, Bsp2095I, Bst19II, BspKT6I, DpnII, MboI, NmeCI, SsiAI | | BstM6I | Bacillus stearothermophilus M6 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, Fsp1604I, MvaI | | BstMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BsoMAI | | BstMBI | Bacillus stearothermophilus MB | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I | | BstMCI | Bacillus stearothermophilus MC | CGRYCG | 4 | | | BstMZ611I | Bacillus stearothermophilus MZ611 | CCNGG | 1 | | | BstNI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, Bst2UI, Fsp1604I, SniI, Sth117I | | Bst31NI | Bacillus stearothermophilus 31N | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, MbiI | | BstNSI | Bacillus stearothermophilus 1161NS | RCATGY | 5 | | | BstNZ169I | Bacillus stearothermophilus NZ169 | ATCGAT | 2 | BanIII, BciBI, BdiI, Bli41I, Bsa29I, BspDI, LplI, Rme21I, SpmI, ZhoI | | BstOI | Bacillus stearothermophilus O22 | CCWGG | 2 | AjnI, ApyI, BciBII, BptI, Bst1I, Bst2UI, Fsp1604I, SniI, Sth117I | | BstOZ616I | Bacillus stearothermophilus OZ616 | GGGAC | 9 | | | BstPI | Bacillus stearothermophilus | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT9I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | | BstPZ418I | | GGATG | 8 | | | BstPZ740I | Bacillus stearothermophilus PZ740 | CTTAAG | 1 | | | BstRZ246I | Bacillus stearothermophilus RZ246 | ATTTAAAT | 4 | | | BstSI | Bacillus stearothermophilus S183 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, NspIII, OfoI, PunAI | | BstSCI | Bacillus stearothermophilus SC | CCNGG | 1 | | | BstSFI | Bacillus stearothermophilus SF | CTRYAG | 1 | | | BstSNI | Bacillus stearothermophilus SN | TACGTA | 3 | | | BstSWI | Bacillus stearothermophilus SW | ATTTAAAT | 4 | | | BstT7I | Bacillus stearothermophilus T7 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, FbaI, Ksp22I,  ParI | | BstT9I | Bacillus stearothermophilus T9 | GGTNACC | 1 | AspAI, Bse64I, BstT10I, BstPI, Eco91I, EcoO128I, NspSAII, PspEI | | BstT10I | Bacillus stearothermophilus T10 | GGTNACC | 1 | AspAI, BseT10I, BstEII, BstT10I, Eco91I, EcoO128I, NspSAII, PspEI | | Bst31TI | Bacillus stearothermophilus 31T | GGATC | 9 | | | BstTS5I | Bacillus stearothermophilus TS5 | GAAGAC | 8 | | | BstUI | Bacillus stearothermophilus U458 | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BtkI, Csp68KVI, FauBII, MvnI, SelI | | Bst2UI | Bacillus stearothermophilus 2U | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, SniI, SslI, TaqXI, ZanI | | BstVI | Bacillus stearothermophilus V | CTCGAG | 1 | BluI, BssHI, MlaAI, PanI, SauLPII, SciI, SlaI, StrI, XhoI | | BstV1I | Bacillus stearothermophilus V1 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I | | BstV2I | Bacillus stearothermophilus V2 | GAAGAC | 8 | | | BstX2I | Bacillus stearothermophilus X2 | RGATCY | 1 | | | BstYI | Bacillus stearothermophilus Y406 | RGATCY | 1 | | | BstZI | Bacillus stearothermophilus Z130 | CGGCCG | 1 | AaaI, BseX3I, EagI, EclXI, Eco52I, SenPT16I, XmaIII | | BstZ17I | Bacillus stearothermophilus 38M | GTATAC | 3 | | | Bsu6I | Bacillus subtilis 6v1 | CTCTTC | 7 | | | Bsu15I | Bacillus subtilis 15 | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, BsuTUI, ClaI | | Bsu23I | Bacillus subtilis 23 | TCCGGA | 1 | AccIII, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | | Bsu36I | Bacillus subtilis 36 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | | Bsu54I | Bacillus subtilis 54 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | | Bsu1532I | Bacillus subtilis 1532 | CGCG | 2 | BceBI, Bpu95I, Bsp123I, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | | Bsu1854I | Bacillus subtilis 1854 | GRGCYC | 5 | | | BsuBI | Bacillus subtilis | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, HalII, Psp23I, PstI, SalPI, SflI, YenI | | BsuFI | Bacillus subtilis | CCGG | 1 | | | BsuMI | Bacillus subtilis 168 | CTCGAG | 1 | XhoI, BssHI, TliI, PaeR7I, Sfr274I, SlaI, StrI | | BsuRI | Bacillus subtilis R | GGCC | 2 | HaeIII | | BsuTUI | Bacillus subtilis TU | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, ClaI | | BteI | Brochothrix thermosphacter | GGCC | 2 | | | BtgI | Bacillus thermoglucosidasius | CCRYGG | 1 | | | BtgZI | Bacillus thermoglucosidasius | GCGATG | 10 | | | BthAI | Bacillus thuringiensis AII | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | | BthCI | Bacillus thuringiensis 2294 | GCNGC | 4 | | | BthDI | Bacillus thuringiensis D4 | CCWGG | 2 | AorI, ApyI, Bse24I, BstNI, BstOI, Bst2UI, CbrI, EcoRII, MvaI, SleI | | BthEI | Bacillus thuringiensis E | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | | BtkI | Bacillus thuringiensis Kumantoensis | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | | BtkII | Bacillus thuringiensis Kumantoensis | GATC | 1 | BfuCI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NmeCI, SauMI | | BtrI | Bacillus stearothermophilus SE-U62 | CACGTC | 3 | | | BtsI | Bacillus thermoglucosidasius | GCAGTG | 8 | | | BveI | Brevundimonas vesicularis RFL1 | ACCTGC | 10 | Acc36I, BfuAI, BspMI | | BvuI | Bacillus vulgatis | GRGCYC | 5 | | | BvuBI | Bacteroides vulgatus | CGTACG | 1 | | | BstI | Bacillus stearothermophilus 1503-4R | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, Nsp29132II | | Bst1I | Bacillus stearothermophilus 1 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | | Bst2I | Bacillus stearothermophilus 2 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, BstOI, Bst2UI, CthII, EcoRII, MvaI | | Bst6I | Bacillus stearothermophilus 6 | CTCTTC | 7 | | | Bst11I | Bacillus stearothermophilus 11 | ACTGG | 6 | | | Bst12I | Bacillus stearothermophilus 12 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst71I, BstV1I | | Bst19I | Bacillus stearothermophilus 19 | GCATC | 9 | | | Bst19II | Bacillus stearothermophilus 19 | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | | Bst28I | Bacillus stearothermophilus 28 | ATCGAT | 2 | BciBI, BdiI, Bli41I, Bsa29I, Bsp106I, BspDI, LplI, SpmI, ZhoI | | Bst38I | Bacillus stearothermophilus 38 | CCWGG | 2 | AorI, BseBI, Bse17I, BsiLI, BspNI, BstOI, Bst2UI, EcoRII, MvaI | | Bst40I | Bacillus stearothermophilus 40 | CCGG | 1 | | | Bst71I | Bacillus stearothermophilus 71 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, BstV1I | | Bst98I | Bacillus stearothermophilus C98 | CTTAAG | 1 | | | Bst100I | Bacillus stearothermophilus 100 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | | Bst1107I | Bacillus stearothermophilus RFL1107 | GTATAC | 3 | | | BstACI | Bacillus stearothermophilus AC | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, HgiDI, Hsp92I | | BstAUI | Bacillus stearothermophilus AU | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, Ssp4800I, SspBI | | BstBI | Bacillus stearothermophilus B225 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, LspI, NspV, SspRFI | | Bst2BI | Bacillus stearothermophilus 2B | CACGAG | 1 | | | BstBAI | Bacillus stearothermophilus BA | YACGTR | 3 | | | BstBSI | Bacillus stearothermophilus BS | GTATAC | 3 | | | BstB7SI | Bacillus stearothermophilus B7S | RCCGGY | 1 | | | BstBS32I | Bacillus stearothermophilus BS32 | GAAGAC | 8 | | | BstBZ153I | Bacillus stearothermophilus BZ153 | GCGCGC | 1 | | | Bst4CI | Bacillus stearothermophilus 4C | ACNGT | 3 | | | BstC8I | Bacillus stearothermophilus C8 | GCNNGC | 3 | | | BstD102I | Bacillus stearothermophilus D102 | CCGCTC | 3 | AccBSI, BsrBI, Bst31NI, MbiI | | BstDEI | Bacillus stearothermophilus DE | CTNAG | 1 | | | BstDSI | Bacillus stearothermophilus DS | CCRYGG | 1 | | | BstEII | Bacillus stearothermophilus ET | GGTNACC | 1 | AcrII, BstPI, BstT9I, BstT10I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | | BstENII | Bacillus stearothermophilus EN | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | | BstEZ359I | Bacillus stearothermophilus EZ359 | GTTAAC | 3 | | | BstFI | Bacillus stearothermophilus FH58 | AAGCTT | 1 | | | BstF5I | Bacillus stearothermophilus F5 | GGATG | 7 | | | BstFNI | Bacillus stearothermophilus | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BstUI, Csp68KVI, FauBII, MvnI, SelI | | BstFZ438I | Bacillus stearothermophilus FZ438 | CCCGC | 9 | | | BstGZ53I | Bacillus stearothermophilus GZ53 | CGTCTC | 7 | | | BstH2I | Bacillus stearothermophilus H2 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, HaeII, LpnI | | BstH9I | Bacillus stearothermophilus H9 | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI,  Bst31TI, BthII, Bth617I, EacI | | BstHHI | Bacillus stearothermophilus HH | GCGC | 3 | AspLEI, BspLAI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | | BstHPI | Bacillus stearothermophilus HP | GTTAAC | 3 | | | BstIZ316I | Bacillus stearothermophilus IZ316 | CACNNNGTG | 6 | AdeI, DraIII | | BstJZ301I | Bacillus stearothermophilus JZ301 | CTNAG | 1 | | | BstKTI | Bacillus stearothermophilus KT | GATC | 3 | AspMDI, Bsp2095I, Bst19II, BspKT6I, DpnII, MboI, NmeCI, SsiAI | | BstM6I | Bacillus stearothermophilus M6 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, Fsp1604I, MvaI | | BstMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BsoMAI | | BstMBI | Bacillus stearothermophilus MB | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I | | BstMCI | Bacillus stearothermophilus MC | CGRYCG | 4 | | | BstMZ611I | Bacillus stearothermophilus MZ611 | CCNGG | 1 | | | BstNI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, Bst2UI, Fsp1604I, SniI, Sth117I | | Bst31NI | Bacillus stearothermophilus 31N | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, MbiI | | BstNSI | Bacillus stearothermophilus 1161NS | RCATGY | 5 | | | BstNZ169I | Bacillus stearothermophilus NZ169 | ATCGAT | 2 | BanIII, BciBI, BdiI, Bli41I, Bsa29I, BspDI, LplI, Rme21I, SpmI, ZhoI | | BstOI | Bacillus stearothermophilus O22 | CCWGG | 2 | AjnI, ApyI, BciBII, BptI, Bst1I, Bst2UI, Fsp1604I, SniI, Sth117I | | BstOZ616I | Bacillus stearothermophilus OZ616 | GGGAC | 9 | | | BstPI | Bacillus stearothermophilus | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT9I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | | BstPZ418I | | GGATG | 8 | | | BstPZ740I | Bacillus stearothermophilus PZ740 | CTTAAG | 1 | | | BstRZ246I | Bacillus stearothermophilus RZ246 | ATTTAAAT | 4 | | | BstSI | Bacillus stearothermophilus S183 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, NspIII, OfoI, PunAI | | BstSCI | Bacillus stearothermophilus SC | CCNGG | 1 | | | BstSFI | Bacillus stearothermophilus SF | CTRYAG | 1 | | | BstSNI | Bacillus stearothermophilus SN | TACGTA | 3 | | | BstSWI | Bacillus stearothermophilus SW | ATTTAAAT | 4 | | | BstT7I | Bacillus stearothermophilus T7 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, FbaI, Ksp22I,  ParI | | BstT9I | Bacillus stearothermophilus T9 | GGTNACC | 1 | AspAI, Bse64I, BstT10I, BstPI, Eco91I, EcoO128I, NspSAII, PspEI | | BstT10I | Bacillus stearothermophilus T10 | GGTNACC | 1 | AspAI, BseT10I, BstEII, BstT10I, Eco91I, EcoO128I, NspSAII, PspEI | | Bst31TI | Bacillus stearothermophilus 31T | GGATC | 9 | | | BstTS5I | Bacillus stearothermophilus TS5 | GAAGAC | 8 | | | BstUI | Bacillus stearothermophilus U458 | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BtkI, Csp68KVI, FauBII, MvnI, SelI | | Bst2UI | Bacillus stearothermophilus 2U | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, SniI, SslI, TaqXI, ZanI | | BstVI | Bacillus stearothermophilus V | CTCGAG | 1 | BluI, BssHI, MlaAI, PanI, SauLPII, SciI, SlaI, StrI, XhoI | | BstV1I | Bacillus stearothermophilus V1 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I | | BstV2I | Bacillus stearothermophilus V2 | GAAGAC | 8 | | | BstX2I | Bacillus stearothermophilus X2 | RGATCY | 1 | | | BstYI | Bacillus stearothermophilus Y406 | RGATCY | 1 | | | BstZI | Bacillus stearothermophilus Z130 | CGGCCG | 1 | AaaI, BseX3I, EagI, EclXI, Eco52I, SenPT16I, XmaIII | | BstZ17I | Bacillus stearothermophilus 38M | GTATAC | 3 | | | Bsu6I | Bacillus subtilis 6v1 | CTCTTC | 7 | | | Bsu15I | Bacillus subtilis 15 | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, BsuTUI, ClaI | | Bsu23I | Bacillus subtilis 23 | TCCGGA | 1 | AccIII, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | | Bsu36I | Bacillus subtilis 36 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | | Bsu54I | Bacillus subtilis 54 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | | Bsu1532I | Bacillus subtilis 1532 | CGCG | 2 | BceBI, Bpu95I, Bsp123I, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | | Bsu1854I | Bacillus subtilis 1854 | GRGCYC | 5 | | | BsuBI | Bacillus subtilis | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, HalII, Psp23I, PstI, SalPI, SflI, YenI | | BsuFI | Bacillus subtilis | CCGG | 1 | | | BsuMI | Bacillus subtilis 168 | CTCGAG | 1 | XhoI, BssHI, TliI, PaeR7I, Sfr274I, SlaI, StrI | | BsuRI | Bacillus subtilis R | GGCC | 2 | HaeIII | | BsuTUI | Bacillus subtilis TU | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, ClaI | | BteI | Brochothrix thermosphacter | GGCC | 2 | | | BtgI | Bacillus thermoglucosidasius | CCRYGG | 1 | | | BtgZI | Bacillus thermoglucosidasius | GCGATG | 10 | | | BthAI | Bacillus thuringiensis AII | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | | BthCI | Bacillus thuringiensis 2294 | GCNGC | 4 | | | BthDI | Bacillus thuringiensis D4 | CCWGG | 2 | AorI, ApyI, Bse24I, BstNI, BstOI, Bst2UI, CbrI, EcoRII, MvaI, SleI | | BthEI | Bacillus thuringiensis E | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | | BtkI | Bacillus thuringiensis Kumantoensis | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | | BtkII | Bacillus thuringiensis Kumantoensis | GATC | 1 | BfuCI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NmeCI, SauMI | | BtrI | Bacillus stearothermophilus SE-U62 | CACGTC | 3 | | | BtsI | Bacillus thermoglucosidasius | GCAGTG | 8 | | | BveI | Brevundimonas vesicularis RFL1 | ACCTGC | 10 | Acc36I, BfuAI, BspMI | | BvuI | Bacillus vulgatis | GRGCYC | 5 | | | BvuBI | Bacteroides vulgatus | CGTACG | 1 | | | CacI | Clostridium acetobutylicum N1-4081 | GATC | 1 | | | Cac8I | Clostridium acetobutylicum ABKn8 | GCNNGC | 3 | | | CaiI | Comamonas acidovarans Iti19-021 | CAGNNNCTG | 6 | AlwNI | | CauI | Chloroflexus aurantiacus | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | | CauII | Chloroflexus aurantiacus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, Eco1831I, EcoHI, Kpn49kII, NciI | | CauB3I | Chloroflexus aurantiacus B3 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BspEI, BspMII, Kpn2I, MroI, PtaI | | CbiI | Clostridium bifermentans B-4 | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, Csp45I, LspI, NspV, SspRFI | | CboI | Clostridium botulinum | CCGG | 1 | | | CbrI | Citrobacter braakii 1146 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI | | CciNI | Curtobacterium citreus | GCGGCCGC | 2 | | | CcoI | Clostridium coccoides B-2 | GCCGGC | 3 | | | CcrI | Caulobacter crescentus CB-13 | CTCGAG | 1 | | | CcuI | Chroococcidiopsis cubana | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, PspPI | | CcyI | Clostridium cylindrosporum | GATC | 1 | BfuCI, Bsp67I, Bst19II, CviAI, FnuCI, MboI, NmeCI, SauMI | | CdiI | Citrobacter freundii RFL2 | CATCG | 4 | | | CelI | Citrobacter freundii RFL6 | GGATCC | 1 | AliI, ApaCI, AsiI, BamHI, CelI, NspSAIV, RspLKII, SolI, Uba4009I | | CelII | Coccochloris elabens 17a | GCTNAGC | 2 | | | CeqI | Corynebacterium equi | GATATC | 3 | | | CflI | Cellulomonas flavigena | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, PaePI, PstI, SalPI, Srl5DI, Sst12I | | CfoI | Clostridium formicoaceticum | GCGC | 3 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, HinP1I, HsoI, HspAI, SciNI | | CfrI | Citrobacter freundii RFL2 | YGGCCR | 1 | | | Cfr6I | Citrobacter freundii RFL6 | CAGCTG | 3 | | | Cfr9I | Citrobacter freundii | CCCGGG | 1 | AhyI, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | | Cfr10I | Citrobacter freundii RFL10 | RCCGGY | 1 | | | Cfr13I | Citrobacter freundii RFL13 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, FmuI, Nsp7121I, PspPI | | Cfr42I | Citrobacter freundii RFL42 | CCGCGG | 4 | SacII, CscI, HgaI | | CfrA4I | Citrobacter freundii A4 | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl2zI, PaePI, PstI, SalPI, Srl5DI, Sst12I | | CfrBI | Citrobacter freundii 4111 | CCWWGG | 1 | | | CfrJ4I | Citrobacter freundii J4 | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI | | CfuI | Caulobacter fusiformis BC-25 | GATC | 2 | | | CfuII | Caulobacter fusiformis BC-25 | CTGCAG | 5 | AjoI, AliAJI, CfuII, HalII, PaePI, Psp23I, PstI, SalPI, Srl5DI, YenI | | ChaI | Corynebacterium halofytica | GATC | 4 | BfuCI, Bsp2095I, BspKT6I BtkII, FnuCI, MboI, NmeCI, SsiAI | | ClaI | Caryophanon latum L | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI | | CltI | Caryophanon latum | GGCC | 2 | | | CpfI | Clostridium perfringens | GATC | 1 | AspMDI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NphI, SauMI | | CpoI | Caseobacter polymorphus | CGGWCCG | 2 | | | CscI | Calothrix scopulorum | CCGCGG | 4 | Cfr42I, SacII, HgaI | | CsiAI | Corynebacterium sp. A | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CspAI, PinAI | | CsiBI | Corynebacterium sp. B | GCGGCCGC | 2 | | | CspI | Corynebacterium sp. | CGGWCCG | 2 | | | Csp6I | Corynebacterium sp. RFL6 | GTAC | 1 | AfaI, CviQI, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | | Csp45I | Clostridium sporogenes | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, FspII, LspI, NspV, SspRFI | | CspAI | Corynebacterium sp. 301 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, PinAI | | CspBI | Corynebacterium sp. B | GCGGCCGC | 2 | | | Csp68KI | Cyanothece sp. BH68K | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, Kzo49I, SmuEI | | Csp68KII | Cyanothece sp. BH68K | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, SviI | | Csp68KIII | Cyanothece sp. BH68K | ATGCAT | 5 | BfrBI, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | | Csp68KVI | Cyanothece sp. BH68K | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | | CspKVI | Cyanothece sp. BH68K | CGCG | 2 | | | CstI | Clostridium sticklandii | CTGCAG | 5 | AjoI, AliAJI, CfrA4I, HalII, MhaAI, Pfl21I, PstI, SflI, Srl5DI, YenI | | CstMI | Corynebacterium striatum M82B | AAGGAG | 12 | — None on May 2010 — | | CthII | Clostridium thermocellum | CCWGG | 2 | ApaORI, BseBI, Bse24I, Bst2UI, BstNI, BstM6I, EcoRII, MvaI | | CviAI | Chlorella NC64A (PBCV-1) | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, SauMI | | CviAII | Chlorella NC64A (PBCV-1) | CATG | 1 | | | CviBI | Chlorella NC64A (NC-1A) | GANTC | 1 | | | CviJI | Chlorella NC64A (IL-3A) | RGCY | 2 | | | CviQI | Chlorella NC64A (NY-2A) | GTAC | 1 | AfaI, Csp6I, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | | CviRI | Chlorella NC64A (XZ-6E) | TGCA | 2 | | | CviRII | Chlorella NC64A (XZ-6E) | GTAC | 1 | AfaI, Csp6I, CviQI, HpyBI, PabI, PlaAII, RsaI, RsaNI, | | CviTI | Chlorella NC64A (CA-1A) | RGCY | 2 | | | CvnI | Chromatium vinosum | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | | DdeI | Desulfovibrio desulfuricans | CTNAG | 1 | | | DmaI | Deleya marina | CAGCTG | 3 | | | DpaI | Deleya pacifica | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, Eco255I, RflFII, ScaI, ZrmI | | DpnI | Diplococcus pneumoniae G41 | GATC | 2 | | | DpnII | Diplococcus pneumoniae G41 | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CpfI, Kzo9I, NdeII, Sth368I | | DraI | Deinococcus radiophilus | TTTAAA | 3 | AhaIII, PauAII, SruI | | DraII | Deinococcus radiophilus | RGGNCCY | 2 | | | DraIII | Deinococcus radiophilus | CACNNNGTG | 6 | AdeI, BstIZ316I | | DsaI | Dactylococcopsis salina | CCRYGG | 1 | | | DsaII | Dactylococcopsis salina | GGCC | 2 | | | DsaIII | Dactylococcopsis salina | RGATCY | 1 | | | DsaIV | Dactylococcopsis salina | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiEI, Kzo49I, SmuEI | | DsaV | Dactylococcopsis salina | CCNGG | 1 | | | EacI | Eubacterium acidaminophilum | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI, BstH9I,  Bst31TI, Bth617I, Ral8I | | EaeI | Enterobacter aerogenes | YGGCCR | 1 | | | Eae46I | Enterobacter aerogenes 46 | CCGCGG | 4 | | | EaeAI | Enterobacter aerogenes | CCCGGG | 1 | AhyI, Cfr9I, EclRI, PaeBI, PspAI, PspALI, XcyI, XmaI, XmaCI | | EagI | Enterobacter agglomerans | CGGCCG | 1 | AaaI, BseX3I, BstZI, EclXI, Eco52I, SenPT16I, XmaIII | | EagBI | Enterobacter agglomerans CBNU45 | CGATCG | 4 | Afa16RI, Afa22MI, BspCI, ErhB9I, NblI, Psu161I, RshI, XorII | | EagMI | Enterobacter agglomerans M3 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | | Eam1104I | Enterobacter amnigenus RFL1104 | CTCTTC | 7 | | | EarI | Enterobacter aerogenes | CTCTTC | 7 | | | EcaI | Enterobacter cloacae | GGTNACC | 1 | AcrII, Bse64I, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | | EciI | Escherichia coli | GGCGGA | 11 | | | Eci125I | Escherichia coli VKM-125 | GGTNACC | 1 | AcrII, AspAI, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | | EclI | Enterobacter cloacae | CAGCTG | 3 | | | Ecl136II | Enterobacter cloacae RFL136 | GAGCTC | 3 | | | EclRI | Enterobacter cloacae R | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, Pac25I, PspAI, PspALI, XcyI, XmaI, XmaCI | | EclXI | Enterobacter cloacae 590 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, Eco52I, SenPT16I, XmaIII | | Ecl18kI | Enterobacter cloacae 18k | CCNGG | 1 | | | Ecl37kI | Enterobacter cloacae 37k | CTGCAG | 5 | AjoI, AliAJI, Ecl2zI, PaePI, Psp23I, PstI, Sag16I, SflI, YenI | | Ecl2zI | Enterobacter cloacae 2z | CTGCAG | 5 | AliAJI, Bsp63I, CfrA4I, PaePI, Pfl21I, PstI, SflI, Sst12I, YenI | | Eco24I | Escherichia coli RFL24 | GRGCYC | 5 | | | Eco31I | Escherichia coli RFL31 | GGTCTC | 7 | | | Eco32I | Escherichia coli RFL32 | GATATC | 3 | | | Eco47I | Escherichia coli RFL47 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | | Eco47III | Escherichia coli RFL47 | AGCGCT | 3 | AfeI, AitI, Aor51H, FunI | | Eco52I | Escherichia coli RFL52 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, SenPT16I, XmaIII | | Eco56I | Escherichia coli RFL56 | GCCGGC | 1 | | | Eco57I | Escherichia coli RFL57 | CTGAAG | 13 | AcuI, BspKT5I | | Eco64I | Escherichia coli RFL64 | GGYRCC | 1 | BanI, BbvBI, BspT107I, BshNI, HgiCI, HgiHI, MspB4I, PfaAI | | Eco72I | Escherichia coli RFL72 | CACGTG | 3 | AcvI, BcoAI, BbrPI, PmaCI, PmlI, PspCI | | Eco78I | Escherichia coli RFL78 | GGCGCC | 3 | | | Eco81I | Escherichia coli RFL81 | CCTNAGG | 2 | AxyI, Bse21I, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | | Eco88I | Escherichia coli RFL88 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BstSI, Eco27kI, NspSAI, PlaAI, PunAI | | Eco91I | Escherichia coli RFL91 | GGTNACC | 1 | Bse64I, BstEII, BstPI, BstT9I, BstT10I, EcaI, Eci125I, NspSAII | | Eco105I | Escherichia coli RFL105 | TACGTA | 3 | | | Eco130I | Escherichia coli RFL130 | CCWWGG | 1 | | | Eco147I | Escherichia coli RFL147 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | | Eco255I | Escherichia coli RFL255 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, RflFII, ScaI, ZrmI | | Eco1831I | Escherichia coli RFL1831 | CCSGG | 1 | AhaI, AseII, AsuC2I, BcnI,  BpuMI, CauII, EcoHI, HgiS22I | | EcoA4I | Escherichia coli A4 | GGTCTC | 7 | | | EcoHI | Escherichia coli HI | CCSGG | 1 | AsuC2I, BcnI, BpuMI, CauII, EcoHI, HgiS22I, Kpn49kII, NciI | | EcoHK31I | Escherichia coli HK31 | YGGCCR | 1 | | | EcoICRI | Escherichia coli 2bT | GAGCTC | 3 | | | Eco75KI | Escherichia coli BKM | GRGCYC | 5 | | | Eco57MI | Escherichia coli RFL57M | CTGRAG | 13 | | | EcoO44I | Escherichia coli O44 Hiromi | GGTCTC | 7 | | | EcoO65I | Escherichia coli K11a | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstPI, BstT9I, EcaI, Eco91I, EcoO128I | | EcoO109I | Escherichia coli H709c | RGGNCCY | 2 | | | EcoO128I | Escherichia coli O128Ly3 | GGTNACC | 1 | AspAI, Bse64I, BstEII, BstT9I, EcaI, EcoO65I, NspSAII, PspEI | | EcoP15I | Escherichia coli P15 | CAGCAG | 11 | | | EcoRI | Escherichia coli RY13 | GAATTC | 1 | | | EcoRII | Escherichia coli R245 | CCWGG | 1 | ApaORI, BseBI, BspNI, BstNI, BstOI, Bst2UI, MvaI, SspAI, ZanI | | EcoRV | Escherichia coli J62 pLG74 | GATATC | 3 | | | EcoT14I | Escherichia coli TB14 | CCWWGG | 1 | | | EcoT22I | Escherichia coli TB22 | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SepI, SspD5II | | EcoT38I | Escherichia coli TH38 | GRGCYC | 5 | | | EcoVIII | Escherichia coli E1585-68 | AAGCTT | 1 | | | Eco13kI | Escherichia coli 13k | CCNGG | 1 | | | Eco21kI | Escherichia coli 21k | CCNGG | 1 | | | Eco27kI | Escherichia coli 27 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, OfoI, PunAI | | Eco29kI | Escherichia coli | CCGCGG | 4 | | | Eco53kI | Escherichia coli 53k | GAGCTC | 3 | | | Eco137kI | Escherichia coli 137k | CCNGG | 1 | | | EgeI | Enterobacter gergoviae NA | GGCGCC | 3 | | | EheI | Erwinia herbicola 9/5 | GGCGCC | 3 | | | ErhI | Erwinia rhaponici B9 | CCWWGG | 1 | | | ErhB9I | Erwinia rhaponici B9 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, NblI, Ple19I, Psu161I, RshI, XorII | | ErhB9II | Erwinia rhaponici B9 | CCWWGG | 1 | | | ErpI | Erwinia rhaponici | GGWCC | 1 | Bme18I, BthAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | | EsaBC3I | Environmental sample BC3 | TCGA | 2 | | | EsaBC4I | Environmental sample BC4 | GGCC | 2 | | | EspI | Eucapsis sp. | GCTNAGC | 2 | | | Esp3I | Erwinia sp. RFL3 | CGTCTC | 7 | | | Esp4I | Erwinia sp. RFL4 | CTTAAG | 1 | | | FalII | Flavobacterium aquatile Ob10 | CGCG | 2 | BepI, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, FalII, SelI, ThaI | | FaqI | Flavobacterium aquatile RFL1 | GGGAC | 9 | | | FatI | Flavobacterium aquatile NL3 | CATG | 1 | | | FauI | Flavobacterium aquatile | CCCGC | 9 | | | FauBII | Flavobacterium aureus B | CGCG | 2 | Bpu95I, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, Csp68KVI, SelI, ThaI | | FauNDI | Flavobacterium aquatile ND | CATATG | 2 | | | FbaI | Flavobacterium balustinum | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, Ksp22I,  ParI | | FblI | Flavobacterium balustinum | GTMKAC | 2 | AccI, XmiI | | FbrI | Flavobacterium breve | GCNGC | 2 | | | FdiI | Fremyella diplosiphon | GGWCC | 1 | Bme18I, BthAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | | FdiII | Fremyella diplosiphon | TGCGCA | 3 | Acc16I, AosI, AviII, FspI, MstI, NsbI, PamI, Pun14627I | | FgoI | Fervidobacterium gondwanense AB39T | CTAG | 1 | | | FmuI | Flavobacterium multivorum | GGNCC | 4 | FmuI AvcI, BavAII, Bce22I, Bsu54I, NspIV, Pde12I, UnbI | | FnuAI | Fusobacterium nucleatum A | GANTC | 1 | | | FnuCI | Fusobacterium nucleatum C | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuEI, MgoI, NphI, SauMI | | FnuDI | Fusobacterium nucleatum D | GGCC | 2 | | | FnuDII | Fusobacterium nucleatum D | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FnuDII, ThaI | | FnuDIII | Fusobacterium nucleatum D | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, HhaI, Hin6I, HinP1I, HspAI, SciNI | | FnuEI | Fusobacterium nucleatum E | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, Sau3AI | | Fnu4HI | Fusobacterium nucleatum 4H | GCNGC | 2 | | | FokI | Flavobacterium okeanokoites | GGATG | 8 | | | FriOI | Flavobacterium sp. O9 | GRGCYC | 5 | | | FseI | Frankia sp. Eu11b | GGCCGGCC | 6 | | | FsiI | Frankia sp. | RAATTY | 1 | AcsI, ApoI,  CfaI, XapI | | FspI | Fischerella sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, MstI, NsbI, PamI, Pun14627I | | FspII | Fischerella sp. | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, Ssp1I, SviI | | Fsp1604I | Flavobacterium sp. I 16-04 | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, SleI | | FspAI | Flexibacter sp. TV-m21K | RTGCGCAY | 4 | | | FspBI | Flavobacterium sp. RFLI | CTAG | 1 | | | Fsp4HI | Flavobacterium sp. 4H | GCNGC | 2 | | | FspMSI | Fischerella sp. | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, HgiBI, HgiEI, Kzo49I, SmuEI | | FssI | Fibrobacter succinogenes S85 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Kzo49I, VpaK11AI | | FunI | Fischerella uniformis | AGCGCT | 3 | AfeI, AitI, Aor51H, Eco47III | | FunII | Fischerella uniformis | GAATTC | 1 | | | GalI | Gluconobacter albidus | CCGCGG | 4 | | | GceI | Gluconobacter cerinus | CCGCGG | 4 | | | GceGLI | Gluconobacter cerinus | CCGCGG | 4 | | | GdiI | Gluconobacter dioxyacetonicus | AGGCCT | 3 | AatI, AspMI, Eco147I, PceI, SarI, Sru30DI, SseBI, SteI, StuI | | GdiII | Gluconobacter dioxyacetonicus | CGGCCR | 1 | | | GstI | Geobacillus stearothermophilus | GGATCC | 1 | | | GsuI | Gluconobacter suboxydans H-15T | CTGGAG | 13 | | | HacI | Halococcus acetoinfaciens | GATC | 1 | Bme12I, Bsp67I, BstENII, CcyI, FnuEI, MgoI, NphI, Sau3AI | | HaeI | Haemophilus aegyptius | WGGCCW | 3 | | | HaeII | Haemophilus aegypticus | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, LpnI | | HaeIII | Haemophilus aegypticus | GGCC | 2 | BsuRI | | HalI | Hafnia alvei B6 | GAATTC | 1 | | | HalII | Hafnia alvei B6 | CTGCAG | 5 | AjoI, AliAJI, Bsp63I, CfrA4I, CfuII, CstI, PstI, SflI, Srl5DI, Sst12I | | HapII | Haemophilus aphrophilus | CCGG | 1 | | | HgaI | Haemophilus gallinarum | GACGC | 8 | | | HgiI | Herpetosiphon giganteus 3303 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiHII, Hin1I, PamII | | HgiAI | Herpetosiphon giganteus HP1023 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI,  Bsm6I, HpyF46II, MspV281I | | HgiBI | Herpetosiphon giganteus Hpg5 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Psp03I, VpaK11AI | | HgiCI | Herpetosiphon giganteus Hpg9 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiHI, MspB4I, PfaAI | | HgiCII | Herpetosiphon giganteus Hpg9 | GGWCC | 1 | Bme18I, BthAI, DsaIV, FspMSI, HgiHIII, Psp03I, VpaK11AI | | HgiCIII | Herpetosiphon giganteus Hpg9 | GTCGAC | 1 | | | HgiDI | Herpetosiphon giganteus Hpa2 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiI, Hin1I, PamII | | HgiDII | Herpetosiphon giganteus Hpa2 | GTCGAC | 1 | | | HgiEI | Herpetosiphon giganteus Hpg24 | GGWCC | 1 | Bme216I, BthAI, DsaIV, ErpI, FspMSI, HgiHIII, VpaK11AI | | HgiGI | Herpetosiphon giganteus Hpa1 | GRCGYC | 2 | AcyI, AosII, BbiII, BstACI, HgiI, HgiGI, Msp17I, PamII | | HgiHI | Herpetosiphon giganteus HP1049 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiCI, MspB4I, PfaAI | | HgiHII | Herpetosiphon giganteus HP1049 | GRCGYC | 2 | AosII, AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Msp17I, PamII | | HgiHIII | Herpetosiphon giganteus HP1049 | GGWCC | 1 | Bme216I, DsaIV, ErpI, HgiBI, Psp03I, VpaK11AI, VpaK11BI | | HgiJI | Herpetosiphon giganteus HFS101 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI | | HgiJII | Herpetosiphon giganteus HFS101 | GRGCYC | 5 | | | HgiS22I | Herpetosiphon giganteus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, CauII, Eco1831I, EcoHI, Kpn49kII | | HhaI | Haemophilus haemolyticus | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, SciNI | | HhaII | Haemophilus haemolyticus | GANTC | 1 | | | Hin1I | Haemophilus influenzae RFL1 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, HgiI, HgiDI, HgiDI, Hsp92I | | Hin1II | Haemophilus influenzae RFL1 | CATG | 4 | | | Hin2I | Haemophilus influenzae RFL2 | CCGG | 1 | | | Hin6I | Haemophilus influenzae RFL6 | GCGC | 1 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, HhaI, HsoI, HspAI, SciNI | | HinJCI | Haemophilus influenzae JC9 | GTYRAC | 3 | | | HinP1I | Haemophilus influenzae P1 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HsoI, HspAI, SciNI | | HincII | Haemophilus influenzae Rc | GTYRAC | 3 | | | HindII | Haemophilus influenzae Rd | GTYRAC | 3 | | | HindIII | Haemophilus influenzae Rd | AAGCTT | 1 | | | HinfI | Haemophilus influenzae Rf | GANTC | 1 | | | HjaI | Hyphomonas jannaschiana | GATATC | 3 | | | HpaI | Haemophilus parainfluenzae | GTTAAC | 3 | | | HpaII | Haemophilus parainfluenzae | CCGG | 1 | | | HphI | Haemophilus parahaemolyticus | GGTGA | 9 | AsuHPI, SspD5I | | Hpy8I | Helicobacter pylori A 8-5 | GTNNAC | 3 | | | Hpy51I | Helicobacter pylori 51 | GTSAC | 1 | | | Hpy99I | Helicobacter pylori J99 | CGWCG | 5 | | | Hpy178III | Helicobacter pylori J178 | TCNNGA | 2 | | | Hpy188I | Helicobacter pylori J188 | TCNGA | 3 | | | Hpy188III | Helicobacter pylori J188 | TCNNGA | 2 | | | HpyAV | Helicobacter pylori 26695 | CCTTC | 9 | | | HpyBI | Helicobacter pylori Roberts | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, PabI, PlaAII, RsaI, RsaNI | | HpyBII | Helicobacter pylori Roberts | GTNNAC | 3 | | | HpyCI | Helicobacter pylori | GATATC | 3 | | | HpyC1I | Helicobacter pylori | CCATC | 9 | | | HpyCH4I | Helicobacter pylori CH4 | CATG | 4 | | | HpyCH4III | Helicobacter pylori CH4 | ACNGT | 3 | | | HpyCH4IV | Helicobacter pylori CH4 | ACGT | 1 | | | HpyCH4V | Helicobacter pylori CH4 | TGCA | 2 | | | HpyF44III | Helicobacter pylori RFL44 | TGCA | 2 | | | HsoI | Haemophilus somnus 2336 | GCGC | 1 | AspLEI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, HspAI, SciNI | | Hsp92I | Haemophilus sp. 92 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, HgiI, HgiDI, HgiHII, Hin1I, Hsp92I | | Hsp92II | Haemophilus sp. 92 | CATG | 4 | | | HspAI | Haemophilus sp. A | GCGC | 1 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, SciNI | | HsuI | Haemophilus suis | AAGCTT | 1 | | | ItaI | Ilyobcater tartaricus | GCNGC | 2 | | | KasI | Kluyvera ascorbata | GGCGCC | 1 | | | Kaz48kI | Klebsiella azeanae | RGGNCCY | 5 | | | KoxII | Klebsiella oxytoca | GRGCYC | 5 | | | KpnI | Klebsiella pneumoniae OK8 | GGTACC | 5 | Acc65I, AhaB8I, Asp718I, SthI | | Kpn2I | Klebsiella pneumoniae RFL2 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | | Kpn378I | Klebsiella pneumoniae 378 | CCGCGG | 4 | | | Kpn2kI | Klebsiella pneumoniae 2k | CCNGG | 1 | | | Kpn49kI | Klebsiella pneumoniae 49k | GAATTC | 1 | | | Kpn49kII | Klebsiella pneumoniae 49k | CCSGG | 1 | AhaI, AsuC2I, BcnI, CauII, EcoHI, HgiS22I, Mgl14481I, NciI, | | KspI | Kluyvera sp. | CCGCGG | 4 | | | Ksp22I | Kurthia sp. 22 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, FbaI,  ParI | | Ksp632I | Kluyvera sp. 632 | CTCTTC | 7 | | | KspAI | Kurthia sp. N88 | GTTAAC | 3 | | | Kzo9I | Kurthia zopfii 9 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstMBI, CpfI, LlaAI, NdeII, Sth368I | | Kzo49I | Kurthia zopfii 49 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI | | LcaI | Lactobacillus casei | ATCGAT | 2 | BdiI, Bli41I, Bsa29I, BscI, Bsp106I, BspDI, Bst28I, LplI, PgaI, ZhoI | | LlaAI | Lactococcus lactis cremoris W9 | GATC | 1 | Bme12I, Bsp67I, BstENII, ChaI, FnuEI, MgoI, NphI, RalF40I | | LlaBI | Lactococcus lactis cremoris W56 | CTRYAG | 1 | | | LlaCI | Lactococcus lactis W15 | AAGCTT | 1 | | | LlaG2I | Lactococcus lactis cremoris | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, PstNHI | | Lmu60I | Listeria murrayi 60 | CCTNAGG | 2 | AocI, AxyI, BspR7I, CvnI, Lmu60I, MstII, SauI, SshAI | | LplI | Lactobacillus plantarum | ATCGAT | 2 | BanIII, BbvAII, BdiI, Bsa29I, BscI, BstNZ169I, ClaI, LcaI, PgaI | | LpnI | Legionella pneumophila | RGCGCY | 3 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, HaeII | | LspI | Lactobacillus sp. | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp45I, PlaII, PpaAI, Ssp1I | | LweI | Listeria welshimeri RFL131 | GCATC | 8 | | | MabI | Microbacterium arborescens SE | ACCWGGT | 1 | | | MaeI | Methanococcus aeolicus PL-15/H | CTAG | 1 | | | MaeII | Methanococcus aeolicus | ACGT | 1 | | | MaeIII | Methanococcus aeolicus | GTNAC | 1 | | | MaeK81I | Microcystis aeruginosa K-81 | CGTACG | 1 | | | MaeK81II | Microcystis aeruginosa | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | | MavI | Mycobacterium avium | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SciI, SlaI, Sol10179I, XhoI | | MbiI | Moraxella bovis Fr1-022 | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, Bst31NI | | MboI | Moraxella bovis | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | | MboII | Moraxella bovis | GAAGA | 9 | | | MchI | Micromonospora chalcea | GGCGCC | 2 | | | MchAI | Mycobacterium chelonei | GCGGCCGC | 2 | | | MchAII | Mycobacterium chelonei | GGCC | 2 | | | McrI | Micrococcus cryophilus | CGRYCG | 4 | | | MfeI | Mycoplasma fermentans | CAATTG | 1 | | | MflI | Microbacterium flavum | RGATCY | 1 | | | MfoAI | Mycobacterium fortuitum TMC 1529 | GGCC | 2 | | | Mgl14481I | Merismopedia glauca 1448-1 | CCSGG | 2 | AseII, AsuC2I, BcnI, BpuMI, CauII, Eco1831I, EcoHI, HgiS22I, NciI | | MgoI | Mycobacterium gordonae | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, NphI, Sau3AI | | MhaAI | Mycobacterium habana 206 | CTGCAG | 5 | AliAJI, Asp713I, Bsp63I, CstI, Ecl37kI, HalII, PaePI, PstI, YenI | | MhlI | Micrococcus halobius SD | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, SduI | | MkrAI | Micrococcus kristinae | GATC | 1 | Bme12I, BspAI, BstENII, ChaI, FnuEI, MgoI, NphI, Sau3AI | | MlaI | Mastigocladus laminosus | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp68KII, LspI, PlaII, Ssp1I | | MlaAI | Micromonospora lacustris | CTCGAG | 1 | BspAAI, BstVI, PanI, SauLPII, Sbi68I, Sfr274I, SlaI, XhoI | | MlsI | Micrococcus luteus Ng 16-122 | TGGCCA | 3 | | | MltI | Micrococcus luteus | AGCT | 2 | AluBI, AluI | | MluI | Micrococcus luteus | ACGCGT | 1 | | | Mlu23I | Micrococcus luteus 23 | GGATCC | 1 | | | Mlu31I | Micrococcus luteus 31 | TGGCCA | 3 | | | MluB2I | Micrococcus luteus B2 | TCGCGA | 3 | | | MluNI | Micrococcus luteus N | TGGCCA | 3 | | | MlyI | Micrococcus lylae | GAGTC | 8 | | | Mly113I | Micrococcus lylae 113 | GGCGCC | 2 | | | MmeI | Methylophilus methylotrophus | TCCRAC | 12 | | | MnlI | Moraxella nonliquefaciens | CCTC | 9 | | | MnoI | Moraxella nonliquefaciens | CCGG | 1 | | | Mph1103I | Moraxella phenylpyruvica RFL1103 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II | | MroI | Micrococcus roseus | TCCGGA | 1 | BbvAIII, BseAI, Bsp13I, BspEI, Bsu23I, CauB3I, PinBII, PtaI | | MroNI | Micrococcus roseus N | GCCGGC | 1 | | | MscI | Micrococcus sp. | TGGCCA | 3 | | | MseI | Micrococcus sp. | TTAA | 1 | | | MspI | Moraxella sp. | CCGG | 1 | | | Msp17I | Micrococcus sp. 17 | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Hin1I, Msp17I, PamII | | Msp20I | Micrococcus sp. | TGGCCA | 3 | | | Msp67I | Micrococcus sp. MS67 | CCNGG | 2 | | | MspA1I | Moraxella sp. A1 | CMGCKG | 3 | | | MspB4I | Moraxella sp. B4 | GGYRCC | 1 | AccB1I, BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, PfaAI | | MspCI | Micrococcus sp. | CTTAAG | 1 | | | MspR9I | Micrococcus sp. R9 | CCNGG | 2 | | | MspSWI | Moraxella sp. SW | ATTTAAAT | 4 | | | MspV281I | Myxosarcinia sp. V/281 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I, BsiHKAI,  Bsm6I, HgiAI,  HpyF46II, | | MspYI | Microcystis sp. J2 | YACGTR | 3 | | | MssI | Methylobacterium sp. Dd 5-732 | GTTTAAAC | 4 | PmeI | | MstI | Microcoleus sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, NsbI, PamI, Pun14627I | | MstII | Microcoleus sp. | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | MthZI | Methanobacterium thermoformicicum Z-245 | CTAG | 1 | | | MunI | Mycoplasma sp. | CAATTG | 1 | | | MvaI | Micrococcus varians RFL19 | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, Bst2UI, SslI, TaqXI, ZanI | | Mva1269I | Micrococcus varians RFL1269 | GAATGC | 7 | Asp26HI, Asp40HI, Asp50HI, BscCI, BsmI, Mva1269I, PctI | | MvnI | Methanococcus vannielii | CGCG | 2 | AccII, Bsh1236I, BstFNI, BtkI, Csp68KVI, FalII, FauBII, ThaI | | MvrI | Micrococcus varians | CGATCG | 4 | Afa22MI, BspCI, EagBI, ErhB9I, Ple19I, PvuI, RshI, XorII | | MxaI | Myxococcus xanthus F18E | GAGCTC | 3 | | | NaeI | Nocardia aerocolonigenes | GCCGGC | 3 | | | NarI | Nocardia argentinensis | GGCGCC | 2 | | | NblI | Nocardia blackwellii | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, MvrI, Ple19I, Psu161I, RshI, XorII | | NciI | Neisseria cinerea | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, EcoHI, HgiS22I, Mgl14481I | | NcoI | Nocardia corallina | CCATGG | 1 | | | NcrI | Nocardia carnea C-212 | AGATCT | 1 | | | NcuI | Neisseria cuniculi | GAAGA | 9 | | | NdaI | Nocardia dassonvillei | GGCGCC | 2 | | | NdeI | Neisseria denitrificans | CATATG | 2 | | | NdeII | Neisseria denitrificans | GATC | 1 | Bce243I, Bsp105I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, Sth368I | | NgoAIII | Neisseria gonorrhoeae FA1090 | CCGCGG | 4 | | | NgoAIV | Neisseria gonorrhoeae FA1090 | GCCGGC | 1 | | | NgoMIV | Neisseria gonorrhoeae MS11 | GCCGGC | 1 | | | NgoPII | Neisseria gonorrhoeae P9-2 | GGCC | 2 | | | NgoPIII | Neisseria gonorrhoeae P9-2 | CCGCGG | 4 | | | NheI | Neisseria mucosa heidelbergensis | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, LlaG2I, PstNHI | | NlaII | Neisseria lactamica | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | | NlaIII | Neisseria lactamica | CATG | 4 | | | NlaIV | Neisseria lactamica | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, PspN4I | | Nli3877I | Nostoc linckia | CYCGRG | 5 | Ama87I, AvaI, BcoI, BsiHKCI, Eco27kI, Eco88I, NspSAI, OfoI | | NmeCI | Neisseria meningitidis C114 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | | NmeRI | Neisseria meningitidis | CAGCTG | 3 | | | NmuCI | Neisseria mucosa C9-2 | GTSAC | 1 | | | NopI | Nocardia opaca | GTCGAC | 1 | | | NotI | Nocardia otitidis-caviarum | GCGGCCGC | 2 | | | NphI | Neisseria pharyngis C245 | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, RalF40I, Sau3AI | | NruI | Nocardia rubra | TCGCGA | 3 | | | NsbI | Neisseria subflava Va-1 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, PamI, Pun14627I | | NsiI | Neisseria sicca | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | | NsiCI | Neisseria sicca C351 | GATATC | 3 | | | NspI | Nostoc sp. C | RCATGY | 5 | | | NspII | Nostoc sp. C | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, MhlI, NspII, SduI | | NspIII | Nostoc sp. C | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, Eco88I, OfoI, PunAI | | NspIV | Nostoc sp. C | GGNCC | 1 | AvcI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | | NspV | Nostoc sp. C | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, PlaII, SspRFI | | Nsp7121I | Nostoc sp. 7121 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | | Nsp29132II | Nostoc sp. | GGATCC | 1 | AliI, ApaCI, BamHI, Bce751I, Nsp29132II, Pfl8I, SolI, Uba4009I | | NspBII | Nostoc sp. | CMGCKG | 3 | | | NspHI | Nostoc sp. | RCATGY | 5 | | | NspLKI | Nocardia sp. LK | GGCC | 2 | | | NspMACI | Nostoc sp. | AGATCT | 1 | | | NspSAI | Nostoc sp. SA | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | | NspSAII | Nostoc sp. SA | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BseT10I, BstPI, Eco91I, NspSAII, PspEI | | NspSAIV | Nostoc sp. SA | GGATCC | 1 | AliI, BamHI, Bsp98I, Bsp4009I, NspSAIV, Pfl8I, SolI, Uba4009I | | NunII | Nocardia uniformis | GGCGCC | 2 | | | OfoI | Oscillatoria foreaui A-1340 | CYCGRG | 1 | AquI, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, PlaAI, PunAI | | OkrAI | Oceanospirillum kriegii | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, BstI, OkrAI, SolI, Uba4009I | | OxaNI | Oerskovia xanthineolytica N | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | PabI | Pyrococcus abyssi | GTAC | 3 | AfaI, Csp6I, CviQI, HpyBI, HpyBI, PlaAII, RsaI,  RsaNI, | | PacI | Pseudomonas alcaligenes | TTAATTAA | 5 | | | Pac25I | Pseudomonas alcaligenes | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PspAI, PspALI, XcyI, XmaI, XmaCI | | PaeI | Pseudomonas aeruginosa | GCATGC | 5 | | | PaeAI | Pseudomonas aeruginosa | CCGCGG | 4 | | | PaeBI | Pseudomonas aeruginosa - 18 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | | PaeHI | Pseudomonas aeruginosa 4148 | GRGCYC | 5 | | | PaeHII | Pseudomonas aeruginosa 4148 | CTGCAG | 5 | AliAJI, BspBI, BspMAI, CfuII, Ecl2zI, HalII, Srl5DI, Sst12I, XcpI | | PaeQI | Pseudomonas aeruginosa Q2 | CCGCGG | 4 | | | PaeR7I | Pseudomonas aeruginosa PA0303 pMG7 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | | Pae2kI | Pseudomonas aeruginosa 2k | AGATCT | 1 | | | Pae5kI | Pseudomonas aeruginosa 5k | CCGCGG | 4 | | | Pae14kI | Pseudomonas aeruginosa 14k | CCGCGG | 4 | | | Pae17kI | Pseudomonas aeruginosa 17k | CAGCTG | 3 | | | Pae18kI | Pseudomonas aeruginosa 18k | AGATCT | 1 | | | PagI | Pseudomonas alcaligenes Sau 14-027 | TCATGA | 1 | | | PalI | Providencia alcalifaciens | GGCC | 2 | | | PamI | Phormidium ambiguum | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, Pun14627I | | PamII | Phormidium ambiguum | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiDI, HgiGI, HgiHII, Hin1I, Hsp92I, Msp17I | | PanI | Pseudomonas alkanolytica | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | | PasI | Pseudomonas anguilliseptica RFL1 | CCCWGGG | 2 | — None on May 2010 — | | PauI | Paracoccus alcaliphilus ZVK3-3 | GCGCGC | 1 | | | PauAI | Phormidium autumnale | RCATGY | 5 | | | PauAII | Phormidium autumnale | TTTAAA | 3 | AhaIII, DraI, SruI | | PceI | Planococcus citreus 55 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | | PciI | Planococcus citreus SE-F45 | ACATGT | 1 | | | PctI | Planococcus citreus SM | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI BmaHI, BsaMI, BscCI, Mva1269I | | Pde12I | Paracoccus denitrificans 12 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | | Pde133I | Paracoccus denitrificans 133 | GGCC | 2 | | | Pde137I | Paracoccus denitrificans 137 | CCGG | 1 | | | PdiI | Pseudomonas diminuta Mck 33-321 | GCCGGC | 3 | | | PfaAI | Phormidium favosum | GGYRCC | 1 | AccB1I, BanI, BbvBI, BshNI, Eco64I, HgiCI, HgiHI, MspB4I | | PfaAII | Phormidium favosum | CATATG | 2 | | | PfaAIII | Phormidium favosum | GCATGC | 5 | | | PfeI | Psychrobacter faecalis RFL1 | GAWTC | 1 | | | Pfl8I | Pseudomonas fluorescens 8 | GGATCC | 1 | AliAJI, BspBI, BsuBI, CflI, CfrA4I, PaePI, Pfl21I, PstI, SflII, Sst12I | | Pfl21I | Pseudomonas sp. 21 | CTGCAG | 5 | | | Pfl23II | Pseudomonas fluorescens RFL23 | CGTACG | 1 | | | Pfl27I | Pseudomonas fluorescens RFL27 | RGGWCCY | 2 | | | PflFI | Pseudomonas fluorescens biotype F | GACNNNGTC | 4 | AspI, AtsI, PsyI, TelI, Tth111I | | PflKI | Pseudomonas fluorescens | GGCC | 2 | | | PfoI | Pseudomonas fluorescens biovar 126 | TCCNGGA | 1 | | | PgaI | Pseudomonas gladioli B4 | ATCGAT | 2 | BanIII, BbvAII, BliAI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | | PhaI | Pasteurella haemolytica | GCATC | 8 | | | PhoI | Pyrococcus horikoshii OT3 | GGCC | 2 | | | PinAI | Pseudomonas inequalis | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, CspAI | | PinBI | Phormidium inundatum | ATGCAT | 5 | EcoT22I, BfrBI, Mph1103I, NsiI, Ppu10I, SepI, SspD5II, Zsp2I | | PinBII | Phormidium inundatum | TCCGGA | 1 | Aor13HI, BlfI, Bsp13I, BspEI, Bsu23I, Kpn2I, PinBII, PtaI | | PlaI | Phormidium lapideum | GGCC | 2 | | | PlaII | Phormidium lapideum | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, SfuI, SspRFI | | PlaAI | Phormidium laminosum | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | | PlaAII | Phormidium laminosum | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, RsaI,  RsaNI, | | PleI | Pseudomonas lemoignei | GAGTC | 9 | | | Ple19I | Pseudomonas lemoignei 19 | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, MvrI, Psu161I, PvuI, RshI, XorII | | PmaCI | Pseudomonas maltophilia CB50P | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmlI, PspCI | | PmeI | Pseudomonas mendocina | GTTTAAAC | 4 | MssI | | Pme55I | Pseudomonas mendocina 55 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI, StuI | | PmlI | Pseudomonas maltophilia | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PspCI | | PovII | Proteus vulgaris | CAGCTG | 3 | | | PpaAI | Phormidium papyraceum | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, SfuI, SspRFI, SviI | | PpaAII | Phormidium papyraceum | TCGA | 1 | | | PpeI | Phormidium persicinum | GGGCCC | 5 | ApaI, Bsp120I, PspOMI | | PpsI | Pseudomonas pseudoalcaligenes PL | GAGTC | 9 | | | Ppu10I | Pseudomonas putida RFL10 | ATGCAT | 1 | BfrBI, Csp68KII, EcoT22I, Mph1103I, NsiI, SepI, SspD5II | | Ppu111I | Pseudomonas putida P111 | GAATTC | 1 | | | PpuAI | Pseudomonas putida A1 | CGTACG | 1 | | | PpuMI | Pseudomonas putida M | RGGWCCY | 2 | | | PpuXI | Pseudomonas putida X | RGGWCCY | 2 | | | PshBI | Plesiomonas shigelloides TPS970 | ATTAAT | 2 | AseI, AsnI, BpoAI, Sru4DI, VspI | | PsiI | Pseudomonas sp. SE-G49 | TTATAA | 3 | | | Psp03I | Phormidium sp. | GGWCC | 4 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11AI | | Psp5II | Pseudomonas sp. RFL5 | RGGWCCY | 2 | | | Psp6I | Pseudomonas sp. B6 | CCWGG | 1 | AeuI, AglI, ApaORI, Bse17I, EcoRII, Fsp1604I, SspAI, Sth117I | | Psp23I | Pseudomonas sp. 23 | CTGCAG | 5 | ApiI, BspBI, CflI, MhaAI, Pfl21I, PstI, SalPI, Sst12I, YenI | | Psp1406I | Pseudomonas pseudoalcaligenes RFL1406 | AACGTT | 2 | AclI | | PspAI | Pseudomonas sp. | CCCGGG | 1 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI, XmaCI | | PspALI | Pseudomonas sp. AL1637 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | | Psp124BI | Pseudomonas sp. 124B | GAGCTC | 5 | | | PspCI | Pseudomonas sp. C | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PmlI | | PspEI | Pseudomonas sp. E | GGTNACC | 1 | AcrII, AspAI, BstEII, BstPI, Eci125I, Eco91I, EcoO65I, EcoO128I | | PspGI | Pyrococcus sp. GI-H | CCWGG | 1 | AeuI, AjnI, AorI, Bse17I, EcoRII, Fsp1604I, Psp6I, SspAI, Sth117I | | PspLI | Pseudomonas sp. L | CGTACG | 1 | | | PspN4I | Pseudomonas sp. N4 | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, NlaIV | | PspOMI | Pseudomonas sp. OM2164 | GGGCCC | 1 | ApaI, Bsp120I, PpeI | | PspPI | Psychrobacter immobilis TA137 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | | PspPPI | Pseudomonas sp. PP | RGGWCCY | 2 | | | PspXI | Pseudomonas sp. A1-1 | VCTCGAGB | 2 | | | PssI | Pseudomonas sp. | RGGNCCY | 5 | | | PstI | Providencia stuartii 164 | CTGCAG | 5 | AliAJI, BspBI, CfuII, Ecl2zI, HalII, PstI, Sag16I, Sag23I, Sst12I, XcpI | | PstNHI | Pseudomonas stutzeri NH | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, LlaG2I | | PsuI | Pseudomonas stutzeri Mck 28-pH52 | RGATCY | 1 | | | Psu161I | Pseudomonas stutzeri 161 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, PvuI, RshI, XorII | | PsuAI | Phormidium subfuscum | YACGTR | 3 | | | PsyI | Pseudomonas syringae Lki 1-pH124 | GACNNNGTC | 4 | AspI, AtsI, PflFI, TelI, Tth111I | | PtaI | Phormidium tadzschicicum | TCCGGA | 1 | Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Kpn2I, PinBII, PtaI | | Pun14627I | Phormidium uncinatum 1462/7 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, PamI | | Pun14627II | Phormidium uncinatum 1462/7 | CAGCTG | 3 | | | PunAI | Phormidium uncinatum | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco27kI, Nli3877I, PlaAI | | PunAII | Phormidium uncinatum | RCATGY | 5 | | | PvuI | Proteus vulgaris | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, NblI, Ple19I, Psu161I, RshI, XorII | | PvuII | Proteus vulgaris | CAGCTG | 3 | | | Pvu84II | Proteus vulgaris 84 | CAGCTG | 3 | | | RalF40I | Ruminococcus albus F-40 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, HacI, MkrAI, Sau3AI, SsiAI | | RcaI | Rhodococcus capsulatum | TCATGA | 1 | | | RflFI | Ruminococcus flavefaciens FD-1 | GTCGAC | 1 | | | RflFII | Ruminococcus flavefaciens FD-1 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, ScaI, ZrmI | | RleAI | Rhizobium leguminosarum | CCCACA | 12 | | | RmaI | Rhodothermus marinus | CTAG | 1 | | | Rme21I | Rhizobium meliloti | ATCGAT | 2 | BanIII, BbvAII, BliRI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | | RsaI | Rhodopseudomonas sphaeroides | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, PlaAII,  RsaNI, | | RshI | Rhodopseudomonas sphaeroides 2.4.1 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, Psu161I, PvuI, XorII | | RspLKI | Rhodococcus sp. LK2 | GCATGC | 5 | | | RspLKII | Rhodococcus sp. LK2 | GGATCC | 1 | AliI, AsiI, BamHI, Bce751I, Nsp29132II, OkrAI, RspLKII, SolI | | RspXI | Rhodococcus sp. | TCATGA | 1 | | | RsrI | Rhodopseudomonas sphaeroides | GAATTC | 1 | | | RsrII | Rhodopseudomonas sphaeroides | CGGWCCG | 2 | | | Rsr2I | Rhodobacter sphaeroides SE-I2 | CGGWCCG | 2 | | | RtrI | Rhizobium trifolii | GTCGAC | 1 | | | Rtr63I | Rhizobium trifolii 63 | GTCGAC | 1 | | | SacI | Streptomyces achromogenes | GAGCTC | 5 | | | SacII | Streptomyces achromogenes | CCGCGG | 4 | Cfr42I | | SacNI | Streptomyces achromogenes N-J-H | GRGCYC | 5 | | | SalI | Streptomyces albus | GTCGAC | 1 | | | SalPI | Streptomyces albus | CTGCAG | 5 | ApiI, BspMAI, CstI, Ecl37kI, Ecl2zI, Psp23I, PstI, Srl5DI, YenI | | SanDI | Streptomyces sp. | GGGWCCC | 2 | | | SapI | Saccharopolyspora sp. | GCTCTTC | 8 | | | SarI | Streptomyces aureomonopodiales | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, Sru30DI, SseBI, SteI, StuI | | SatI | Staphylococcus arlettae RFL832 | GCNGC | 2 | | | SauI | Streptomyces aureofaciens IKA 18/4 | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | Sau96I | Staphylococcus aureus PS96 | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | | Sau3239I | Streptomyces aureofaciens | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | | Sau3AI | Staphylococcus aureus 3A | GATC | 1 | Bce243I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | | SauBMKI | Streptomyces aureofaciens BM-K | GCCGGC | 3 | | | SauHPI | Streptomyces aureofaciens R8/26 | GCCGGC | 3 | | | SauLPI | Streptomyces aureofaciens B-96 | GCCGGC | 3 | | | SauLPII | Streptomyces aureofaciens B-96 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | | SauMI | Staphylococcus aureus M | GATC | 1 | BscFI, BspAI, BstKTI, ChaI, HacI, MkrAI, RalF40I, SsiAI | | SauNI | Streptomyces aureofaciens NMU | GCCGGC | 3 | | | SauSI | Streptomyces aureofaciens 16 | GCCGGC | 3 | | | SbfI | Streptomyces sp. BF-61 | CCTGCAGG | 6 | | | Sbi68I | Streptomyces bikiniensis JAM68 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | | Sbo13I | Shigella boydii 13 | TCGCGA | 3 | | | SbvI | Streptococcus bovis II/1 | GGCC | 2 | | | ScaI | Streptomyces caespitosus | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ZrmI | | SceIII | Saccharomyces cerevisiae | GCCGGC | 1 | | | SchI | Staphylococcus cohnii Lki 19-320 | GAGTC | 8 | | | SchZI | Streptomyces chusanensis ZS-2 | CCGCGG | 4 | | | SciI | Streptoverticillium cinnamoneum | CTCGAG | 3 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SlaI, Sol10179I, XhoI | | SciNI | Spiroplasma citri ASP2 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI | | ScrFI | Streptococcus cremoris F | CCNGG | 2 | | | SdaI | Streptomyces diastaticus Ng7-324 | CCTGCAGG | 6 | | | SduI | Streptococcus durans RFL3 | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII | | SecI | Synechocystis sp. 6701 | CCNNGG | 1 | | | SelI | Synechococcus elongatus | CGCG | 1 | AccII, Bsh1236I, Bsp123I, Bsp50I, BstFNI, BstUI, BtkI, Csp68KVI | | SenPT16I | Salmonella enteritidis PT16 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, XmaIII | | SenPT14bI | Salmonella enteritidis PT14b | CCGCGG | 4 | | | SepI | Staphylococcus epidermidis | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | | SexAI | Streptomyces exfoliatus | ACCWGGT | 1 | | | SexBI | Streptomyces exfoliatus | CCGCGG | 4 | | | SexCI | Streptomyces exfoliatus | CCGCGG | 4 | | | SfaI | Streptococcus faecalis zymogenes | GGCC | 2 | | | SfaNI | Streptococcus faecalis ND547 | GCATC | 8 | | | SfcI | Streptococcus faecium | CTRYAG | 1 | | | SfeI | Streptococcus faecalis | CTRYAG | 1 | | | SflI | Streptoverticillium flavopersicum | CTGCAG | 5 | ApiI, BspMAI, BsuBI, CfrA4I, Psp23I, PstI, Sag23I, Srl5DI, YenI | | SfoI | Serratia fonticola | GGCGCC | 3 | | | Sfr274I | Streptomyces fradiae 274 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | | Sfr303I | Streptomyces fradiae 303 | CCGCGG | 4 | | | SfuI | Streptomyces fulvissimus | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, PlaII, Ssp1I, SviI | | SgfI | Streptomyces griseoruber | GCGATCGC | 5 | AsiSI,  RgaI, SfaAI | | SgrAI | Streptomyces griseus | CRCCGGYG | 2 | | | SgrBI | Streptomyces griseus | CCGCGG | 4 | | | SimI | Staphylococcus intermedius 6H | GGGTC | 2 | | | SinI | Salmonella infantis | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | | SlaI | Streptomyces lavendulae | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | | SleI | Synechococcus leopoliensis | CCWGG | 1 | AeuI, AglI, ApaORI, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | | Slu1777I | Streptomyces lusitanus 1777 | GCCGGC | 3 | | | SmaI | Serratia marcescens Sb | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | | SmiI | Streptococcus milleri S | ATTTAAAT | 4 | | | SmlI | Stenotrophomonas maltophilia | CTYRAG | 1 | | | SmuI | Sphingobacterium multivorum RFL21 | CCCGC | 9 | | | SmuEI | Streptococcus mutans E | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | | SnaBI | Sphaerotilus natans | TACGTA | 3 | | | SniI | Streptomyces niveus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, MvaI, SspAI | | SnoI | Streptomyces novocastria | GTGCAC | 1 | Alw44I, ApaLI, VneI | | SolI | Streptoverticillium olivoverticillatum | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, Bce751I, CelI, OkrAI, SolI, SurI | | Sol10179I | Streptomyces olivochromogenes ST10179 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | | SpaHI | Synechococus parietina | GCATGC | 5 | | | SpeI | Sphaerotilus natans | ACTAGT | 1 | AhII, AclNI, BcuI | | SphI | Streptomyces phaeochromogenes | GCATGC | 5 | | | SplI | Spirulina platensis | CGTACG | 1 | | | SpmI | Sphingobacterium multivorum RFL21 | ATCGAT | 2 | BanIII, BbvAII, BdiI, BscI, Bsa29I, BspJI, ClaI, LcaI, PgaI, Ssp27144I | | SpoI | Salmonella potsdam | TCGCGA | 3 | | | SpuI | Streptomyces pulveraceus | CCGCGG | 4 | | | SrfI | Streptomyces sp. | GCCCGGGC | 4 | | | SrlI | Selenomonas ruminantium lactilytica 84 | GCCGGC | 1 | | | Srl5DI | Selenomonas ruminantium 5 | CTGCAG | 5 | AliAJI, Asp713I, BspMAI, BsuBI, CfrA4I, Pfl21I, PstI, SflI, Srl5DI | | Srl32DII | Selenomonas ruminantium 32 | GAATTC | 1 | | | Srl55DI | Selenomonas ruminantium lactilytica 55 | GAATTC | 1 | | | Srl56DI | Selenomonas ruminantium 56 | CTRYAG | 1 | | | SruI | Selenomonas ruminantium 18D | TTTAAA | 3 | AhaIII, DraI, PauAII | | Sru4DI | Selenomonas ruminantium | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, VspI | | Sru30DI | Selenomonas ruminantium 30 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, SseBI, SteI, StuI | | SsbI | Streptomyces scabies | AAGCTT | 1 | | | SscL1I | Staphylococcus sp. L1 | GANTC | 1 | | | Sse9I | Sporosarcina sp. 9 | AATT | 1 | | | Sse232I | Streptomyces sp. RH232 | CGCCGGCG | 2 | | | Sse1825I | Streptomyces sp. | GGGWCCC | 2 | | | Sse8387I | Streptomyces sp. 8387 | CCTGCAGG | 6 | | | Sse8647I | Streptomyces sp. | AGGWCCT | 2 | | | SseAI | Streptomyces sp. | GGCGCC | 2 | | | SseBI | Streptomyces sp. | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SteI, StuI | | SshAI | Salmonella shikmonah | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | SsiI | Staphylococcus sciuri RFL1 | CCGC | 1 | AciI | | SsiAI | Staphylococcus sp. A | GATC | 1 | BscFI, BspAI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | | SsiBI | Staphylococcus sp. B | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | | SslI | Streptococcus salivarius thermophilus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, MvaI | | SsoI | Shigella sonnei 47 | GAATTC | 1 | | | SsoII | Shigella sonnei 47 | CCNGG | 1 | | | SspI | Sphaerotilus sp. | AATATT | 3 | | | Ssp1I | Streptomyces sp. RFL1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PlaII, SfuI, SspRFI, SviI | | Ssp4800I | Streptomyces sp. BMTU 4800 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, SspBI | | Ssp5230I | Streptomyces sp. 5230 | GACGTC | 5 | AatII, ZraI | | Ssp27144I | Synechococcus sp. | ATCGAT | 2 | BanIII, BavCI, BbvAII, BscI, BspJI, BspOVII, BstNZ169I, ClaI, LcaI | | SspAI | Synechococcus sp. | CCWGG | 1 | AeuI, AorI, Bse17I, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | | SspBI | Streptomyces sp. | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, Ssp4800I | | SspCI | Streptomyces sp. | GCCGGC | 3 | | | SspD5I | Staphylococcus sp. D5 | GGTGA | 8 | AsuHPI, HphI | | SspD5II | Staphylococcus sp. D5 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SepI, Zsp2I | | SspRFI | Synechococcus sp. RF-1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I, SviI | | SsrI | Staphylococcus saprophyticus B6 | GTTAAC | 3 | | | SstI | Streptomyces stanford | GAGCTC | 5 | | | SstII | Streptomyces stanford | CCGCGG | 4 | | | Sst12I | Streptomyces sp. ST-12 | CTGCAG | 5 | Asp713I, BloHII, BspMAI, BsuBI, CfuII, Psp23I, PstI, SflI, Srl5DI | | SteI | Streptomyces tendae | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, StuI | | SthI | Salmonella thompson YY356 | GGTACC | 1 | Acc65I, AhaB8I, Asp718I, KpnI, | | Sth117I | Streptococcus thermophilus ST117 | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, EcoRII, MvaI, SspAI | | Sth132I | Streptococcus thermophilus | CCCG | 8 | | | Sth134I | Streptococcus thermophilus 134 | CCGG | 1 | | | Sth368I | Streptococcus thermophilus CNRZ368 | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | | StrI | Streptomyces thermodiastaticus | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | | StsI | Streptococcus sanguis 54 | GGATG | 9 | | | StuI | Streptomyces tubercidicus | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI | | StyI | Salmonella typhi | CCWWGG | 1 | | | StyD4I | Salmonella typhi D4 | CCNGG | 1 | | | SuaI | Sulfolobus acidocaldarius | GGCC | 2 | | | SuiI | Sulfolobus islandicus REN2HI | GCWGC | 1 | AceI, ApeKI, Taq52I, TseI | | SunI | Synechococcus uniformis | CGTACG | 1 | | | SurI | Sporosarcina ureae 2 | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, OkrAI, RspLKII, SolI | | SviI | Streptomyces violochromogenes | TTCGAA | 2 | AsuII, Bpu14I, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I | | SwaI | Staphylococcus warneri | ATTTAAAT | 4 | | | TaaI | Thermus aquaticus Vn 4-311 | ACNGT | 3 | | | TaiI | Thermus aquaticus cs1-331 | ACGT | 4 | | | TaqI | Thermus aquaticus | TCGA | 1 | | | TaqII | Thermus aquaticus YTI | GACCGA | 11 | | | Taq52I | Thermus aquaticus YS52 | GCWGC | 1 | AceI, ApeKI, SuiI, TseI | | TaqXI | Thermus aquaticus | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, MvaI, SleI, SspAI | | TasI | Thermus aquaticus Vn 4-211 | AATT | 1 | | | TatI | Thermus aquaticus CBA1-331 | WGTACW | 1 | | | TauI | Thermus aquaticus | GCSGC | 4 | | | TelI | Tolypothrix elabens | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, Tth111I | | TfiI | Thermus filiformis | GAWTC | 1 | | | ThaI | Thermoplasma acidophilum | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FalII, FnuDII | | TliI | Thermococcus litoralis | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, StrI, XhoI | | Tru1I | Thermus ruber RFL1 | TTAA | 1 | | | Tru9I | Thermus ruber 9 | TTAA | 1 | | | Tru201I | Thermus ruber 201 | RGATCY | 1 | | | TscI | Thermus sp. 491A | ACGT | 4 | | | TseI | Thermus sp. 93170 | GCWGC | 1 | AceI, ApeKI, SuiI, Taq52I | | Tsp1I | Thermus sp. 1 | ACTGG | 6 | | | Tsp32I | Thermus sp. 32 | TCGA | 1 | | | Tsp32II | Thermus sp. 32 | TCGA | 1 | | | Tsp45I | Thermus sp. YS45 | GTSAC | 1 | | | Tsp49I | Thermus sp. | ACGT | 4 | | | Tsp509I | Thermus sp. | AATT | 1 | | | TspBI | Thermophilic sp. | CCRYGG | 1 | | | Tsp4CI | Thermus sp. 4C | ACNGT | 3 | | | TspDTI | Thermus sp. DT | ATGAA | 10 | — None on May 2010 — | | TspEI | Thermus sp. 1E | AATT | 1 | | | TspGWI | Thermus sp. GW | ACGGA | 10 | | | TspMI = UthSI | Unidentified thermophile | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, SmaI, XcyI, XmaI, XmaCI | | TspRI | Thermus sp. R | CASTGNN | 7 | | | Tth111I | Thermus thermophilus 111 | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, TelI | | Tth111II | Thermus thermophilus 111 | CAARCA | 11 | | | TthHB8I | Thermus thermophilus HB8 | TCGA | 1 | | | Uba4009I | Unidentified bacterium A | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, RspLKII, SolI | | Uba153AI | Unidentified bacterium 153A | CAGCTG | 3 | | | UbaM39I | Unidentified bacterium M39 | CAGCTG | 3 | | | UnbI | Unidentified bacterium #8 | GGNCC | 1 | AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV, UnbI | | Uur960I | Ureaplasma urealyticum 960 | GCNGC | 2 | | | Vha464I | Vibrio harveyi 464 | CTTAAG | 1 | | | VneI | Vibrio nereis 18 | GTGCAC | 1 | Alw44I, ApaLI, SnoI | | VpaK32I | Vibrio parahaemolyticus 4387-61 | GCTCTTC | 8 | | | VpaK11AI | Vibrio parahaemolyticus 1743 | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11BI | | VpaK11BI | Vibrio parahaemolyticus 1743-1 | GGWCC | 1 | BsrAI, CauI, EagMI, FdiI, HgiBI, HgiJI, SinI, VpaK11AI | | VspI | Vibrio sp. 343 | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, Sru4DI | | XapI | Xanthomonas ampelina Slo 51-021 | RAATTY | 1 | AcsI, ApoI,  CfaI, FsiI | | XbaI | Xanthomonas badrii | TCTAGA | 1 | | | XcaI | Xanthomonas campestris | GTATAC | 3 | | | XceI | Xanthomonas campestris Ast 40-024 | RCATGY | 5 | | | XciI | Xanthomonas citri | GTCGAC | 1 | | | XcyI | Xanthomonas cyanopsidis 13D5 | CCCGGG | 1 | CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XmaI, XmaCI | | XhoI | Xanthomonas holcicola | CTCGAG | 1 | AbrI, BluI, BssHI, PanI, Sau3239I, Sfr274I, TliI, XpaI | | XhoII | Xanthomonas holcicola | RGATCY | 1 | | | XmaI | Xanthomonas malvacearum | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, TspMI, XcyI, XmaCI | | XmaIII | Xanthomonas malvacearum | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, SenPT16I | | XmaCI | Xanthomonas malvacearum C | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, Pac25I, PspAI, TspMI, XcyI, XmaI | | XmaJI | Xanthomonas maltophilia Jo 85-025 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, BspA2I | | XmiI | Xanthomonas maltophilia Jo 21-021 | GTMKAC | 2 | AccI, FblI | | XorII | Xanthomonas oryzae | CGATCG | 4 | Afa16RI, BspCI, EagBI, ErhB9I, MvrI, Ple19I, PvuI, RshI | | XpaI | Xanthomonas papavericola | CTCGAG | 1 | BssHI, MavI, PanI, SauLPII, Sbi68I, Sol10179I, StrI, XhoI | | XspI | Xanthomonas sp. YK1 | CTAG | 1 | | | YenI | Yersinia enterocolitica 08 A2635 | CTGCAG | 5 | Asp713I, BsuBI, CfrA4I, Ecl37kI, Psp23I, PstI, SalPI, SflI, Sst12I | | ZanI | Zymomonas anaerobia | CCWGG | 2 | ApaORI, BseBI, BspNI, BstNI, Bst2UI, CthII, EcoRII, MvaI, SspAI | | ZhoI | Zymomonas holcicola | ATCGAT | 2 | BanIII, BbvAII, BscI, BspJI, ClaI, LcaI, PgaI, SpmI, Ssp27144I | | ZraI | Zoogloea ramigera 11 | GACGTC | 3 | AatII, Ssp5230I | | ZrmI | Zoogloea ramigera SCA | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ScaI | | Zsp2I | Zoogloea sp. 2 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II |","Markdown" "Bioengineering","telatin/seqfu2","re/C-D.md",".md","11862","76","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:----------|:-----------------------------------|:-----------------------|------:|:----------------------------------------------------------------------| | CacI | Clostridium acetobutylicum N1-4081 | GATC | 1 | | | Cac8I | Clostridium acetobutylicum ABKn8 | GCNNGC | 3 | | | CaiI | Comamonas acidovarans Iti19-021 | CAGNNNCTG | 6 | AlwNI | | CauI | Chloroflexus aurantiacus | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | | CauII | Chloroflexus aurantiacus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, Eco1831I, EcoHI, Kpn49kII, NciI | | CauB3I | Chloroflexus aurantiacus B3 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BspEI, BspMII, Kpn2I, MroI, PtaI | | CbiI | Clostridium bifermentans B-4 | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, Csp45I, LspI, NspV, SspRFI | | CboI | Clostridium botulinum | CCGG | 1 | | | CbrI | Citrobacter braakii 1146 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI | | CciNI | Curtobacterium citreus | GCGGCCGC | 2 | | | CcoI | Clostridium coccoides B-2 | GCCGGC | 3 | | | CcrI | Caulobacter crescentus CB-13 | CTCGAG | 1 | | | CcuI | Chroococcidiopsis cubana | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, PspPI | | CcyI | Clostridium cylindrosporum | GATC | 1 | BfuCI, Bsp67I, Bst19II, CviAI, FnuCI, MboI, NmeCI, SauMI | | CdiI | Citrobacter freundii RFL2 | CATCG | 4 | | | CelI | Citrobacter freundii RFL6 | GGATCC | 1 | AliI, ApaCI, AsiI, BamHI, CelI, NspSAIV, RspLKII, SolI, Uba4009I | | CelII | Coccochloris elabens 17a | GCTNAGC | 2 | | | CeqI | Corynebacterium equi | GATATC | 3 | | | CflI | Cellulomonas flavigena | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, PaePI, PstI, SalPI, Srl5DI, Sst12I | | CfoI | Clostridium formicoaceticum | GCGC | 3 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, HinP1I, HsoI, HspAI, SciNI | | CfrI | Citrobacter freundii RFL2 | YGGCCR | 1 | | | Cfr6I | Citrobacter freundii RFL6 | CAGCTG | 3 | | | Cfr9I | Citrobacter freundii | CCCGGG | 1 | AhyI, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | | Cfr10I | Citrobacter freundii RFL10 | RCCGGY | 1 | | | Cfr13I | Citrobacter freundii RFL13 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, FmuI, Nsp7121I, PspPI | | Cfr42I | Citrobacter freundii RFL42 | CCGCGG | 4 | SacII, CscI, HgaI | | CfrA4I | Citrobacter freundii A4 | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl2zI, PaePI, PstI, SalPI, Srl5DI, Sst12I | | CfrBI | Citrobacter freundii 4111 | CCWWGG | 1 | | | CfrJ4I | Citrobacter freundii J4 | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI | | CfuI | Caulobacter fusiformis BC-25 | GATC | 2 | | | CfuII | Caulobacter fusiformis BC-25 | CTGCAG | 5 | AjoI, AliAJI, CfuII, HalII, PaePI, Psp23I, PstI, SalPI, Srl5DI, YenI | | ChaI | Corynebacterium halofytica | GATC | 4 | BfuCI, Bsp2095I, BspKT6I BtkII, FnuCI, MboI, NmeCI, SsiAI | | ClaI | Caryophanon latum L | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI | | CltI | Caryophanon latum | GGCC | 2 | | | CpfI | Clostridium perfringens | GATC | 1 | AspMDI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NphI, SauMI | | CpoI | Caseobacter polymorphus | CGGWCCG | 2 | | | CscI | Calothrix scopulorum | CCGCGG | 4 | Cfr42I, SacII, HgaI | | CsiAI | Corynebacterium sp. A | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CspAI, PinAI | | CsiBI | Corynebacterium sp. B | GCGGCCGC | 2 | | | CspI | Corynebacterium sp. | CGGWCCG | 2 | | | Csp6I | Corynebacterium sp. RFL6 | GTAC | 1 | AfaI, CviQI, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | | Csp45I | Clostridium sporogenes | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, FspII, LspI, NspV, SspRFI | | CspAI | Corynebacterium sp. 301 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, PinAI | | CspBI | Corynebacterium sp. B | GCGGCCGC | 2 | | | Csp68KI | Cyanothece sp. BH68K | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, Kzo49I, SmuEI | | Csp68KII | Cyanothece sp. BH68K | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, SviI | | Csp68KIII | Cyanothece sp. BH68K | ATGCAT | 5 | BfrBI, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | | Csp68KVI | Cyanothece sp. BH68K | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | | CspKVI | Cyanothece sp. BH68K | CGCG | 2 | | | CstI | Clostridium sticklandii | CTGCAG | 5 | AjoI, AliAJI, CfrA4I, HalII, MhaAI, Pfl21I, PstI, SflI, Srl5DI, YenI | | CstMI | Corynebacterium striatum M82B | AAGGAG | 12 | — None on May 2010 — | | CthII | Clostridium thermocellum | CCWGG | 2 | ApaORI, BseBI, Bse24I, Bst2UI, BstNI, BstM6I, EcoRII, MvaI | | CviAI | Chlorella NC64A (PBCV-1) | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, SauMI | | CviAII | Chlorella NC64A (PBCV-1) | CATG | 1 | | | CviBI | Chlorella NC64A (NC-1A) | GANTC | 1 | | | CviJI | Chlorella NC64A (IL-3A) | RGCY | 2 | | | CviQI | Chlorella NC64A (NY-2A) | GTAC | 1 | AfaI, Csp6I, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | | CviRI | Chlorella NC64A (XZ-6E) | TGCA | 2 | | | CviRII | Chlorella NC64A (XZ-6E) | GTAC | 1 | AfaI, Csp6I, CviQI, HpyBI, PabI, PlaAII, RsaI, RsaNI, | | CviTI | Chlorella NC64A (CA-1A) | RGCY | 2 | | | CvnI | Chromatium vinosum | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | | DdeI | Desulfovibrio desulfuricans | CTNAG | 1 | | | DmaI | Deleya marina | CAGCTG | 3 | | | DpaI | Deleya pacifica | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, Eco255I, RflFII, ScaI, ZrmI | | DpnI | Diplococcus pneumoniae G41 | GATC | 2 | | | DpnII | Diplococcus pneumoniae G41 | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CpfI, Kzo9I, NdeII, Sth368I | | DraI | Deinococcus radiophilus | TTTAAA | 3 | AhaIII, PauAII, SruI | | DraII | Deinococcus radiophilus | RGGNCCY | 2 | | | DraIII | Deinococcus radiophilus | CACNNNGTG | 6 | AdeI, BstIZ316I | | DsaI | Dactylococcopsis salina | CCRYGG | 1 | | | DsaII | Dactylococcopsis salina | GGCC | 2 | | | DsaIII | Dactylococcopsis salina | RGATCY | 1 | | | DsaIV | Dactylococcopsis salina | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiEI, Kzo49I, SmuEI | | DsaV | Dactylococcopsis salina | CCNGG | 1 | |","Markdown" "Bioengineering","telatin/seqfu2","re/S.md",".md","21577","134","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:----------|:---------------------------------------|:-----------------------|------:|:-----------------------------------------------------------------------| | SacI | Streptomyces achromogenes | GAGCTC | 5 | | | SacII | Streptomyces achromogenes | CCGCGG | 4 | Cfr42I | | SacNI | Streptomyces achromogenes N-J-H | GRGCYC | 5 | | | SalI | Streptomyces albus | GTCGAC | 1 | | | SalPI | Streptomyces albus | CTGCAG | 5 | ApiI, BspMAI, CstI, Ecl37kI, Ecl2zI, Psp23I, PstI, Srl5DI, YenI | | SanDI | Streptomyces sp. | GGGWCCC | 2 | | | SapI | Saccharopolyspora sp. | GCTCTTC | 8 | | | SarI | Streptomyces aureomonopodiales | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, Sru30DI, SseBI, SteI, StuI | | SatI | Staphylococcus arlettae RFL832 | GCNGC | 2 | | | SauI | Streptomyces aureofaciens IKA 18/4 | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | Sau96I | Staphylococcus aureus PS96 | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | | Sau3239I | Streptomyces aureofaciens | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | | Sau3AI | Staphylococcus aureus 3A | GATC | 1 | Bce243I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | | SauBMKI | Streptomyces aureofaciens BM-K | GCCGGC | 3 | | | SauHPI | Streptomyces aureofaciens R8/26 | GCCGGC | 3 | | | SauLPI | Streptomyces aureofaciens B-96 | GCCGGC | 3 | | | SauLPII | Streptomyces aureofaciens B-96 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | | SauMI | Staphylococcus aureus M | GATC | 1 | BscFI, BspAI, BstKTI, ChaI, HacI, MkrAI, RalF40I, SsiAI | | SauNI | Streptomyces aureofaciens NMU | GCCGGC | 3 | | | SauSI | Streptomyces aureofaciens 16 | GCCGGC | 3 | | | SbfI | Streptomyces sp. BF-61 | CCTGCAGG | 6 | | | Sbi68I | Streptomyces bikiniensis JAM68 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | | Sbo13I | Shigella boydii 13 | TCGCGA | 3 | | | SbvI | Streptococcus bovis II/1 | GGCC | 2 | | | ScaI | Streptomyces caespitosus | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ZrmI | | SceIII | Saccharomyces cerevisiae | GCCGGC | 1 | | | SchI | Staphylococcus cohnii Lki 19-320 | GAGTC | 8 | | | SchZI | Streptomyces chusanensis ZS-2 | CCGCGG | 4 | | | SciI | Streptoverticillium cinnamoneum | CTCGAG | 3 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SlaI, Sol10179I, XhoI | | SciNI | Spiroplasma citri ASP2 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI | | ScrFI | Streptococcus cremoris F | CCNGG | 2 | | | SdaI | Streptomyces diastaticus Ng7-324 | CCTGCAGG | 6 | | | SduI | Streptococcus durans RFL3 | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII | | SecI | Synechocystis sp. 6701 | CCNNGG | 1 | | | SelI | Synechococcus elongatus | CGCG | 1 | AccII, Bsh1236I, Bsp123I, Bsp50I, BstFNI, BstUI, BtkI, Csp68KVI | | SenPT16I | Salmonella enteritidis PT16 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, XmaIII | | SenPT14bI | Salmonella enteritidis PT14b | CCGCGG | 4 | | | SepI | Staphylococcus epidermidis | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | | SexAI | Streptomyces exfoliatus | ACCWGGT | 1 | | | SexBI | Streptomyces exfoliatus | CCGCGG | 4 | | | SexCI | Streptomyces exfoliatus | CCGCGG | 4 | | | SfaI | Streptococcus faecalis zymogenes | GGCC | 2 | | | SfaNI | Streptococcus faecalis ND547 | GCATC | 8 | | | SfcI | Streptococcus faecium | CTRYAG | 1 | | | SfeI | Streptococcus faecalis | CTRYAG | 1 | | | SflI | Streptoverticillium flavopersicum | CTGCAG | 5 | ApiI, BspMAI, BsuBI, CfrA4I, Psp23I, PstI, Sag23I, Srl5DI, YenI | | SfoI | Serratia fonticola | GGCGCC | 3 | | | Sfr274I | Streptomyces fradiae 274 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | | Sfr303I | Streptomyces fradiae 303 | CCGCGG | 4 | | | SfuI | Streptomyces fulvissimus | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, PlaII, Ssp1I, SviI | | SgfI | Streptomyces griseoruber | GCGATCGC | 5 | AsiSI,  RgaI, SfaAI | | SgrAI | Streptomyces griseus | CRCCGGYG | 2 | | | SgrBI | Streptomyces griseus | CCGCGG | 4 | | | SimI | Staphylococcus intermedius 6H | GGGTC | 2 | | | SinI | Salmonella infantis | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | | SlaI | Streptomyces lavendulae | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | | SleI | Synechococcus leopoliensis | CCWGG | 1 | AeuI, AglI, ApaORI, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | | Slu1777I | Streptomyces lusitanus 1777 | GCCGGC | 3 | | | SmaI | Serratia marcescens Sb | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | | SmiI | Streptococcus milleri S | ATTTAAAT | 4 | | | SmlI | Stenotrophomonas maltophilia | CTYRAG | 1 | | | SmuI | Sphingobacterium multivorum RFL21 | CCCGC | 9 | | | SmuEI | Streptococcus mutans E | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | | SnaBI | Sphaerotilus natans | TACGTA | 3 | | | SniI | Streptomyces niveus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, MvaI, SspAI | | SnoI | Streptomyces novocastria | GTGCAC | 1 | Alw44I, ApaLI, VneI | | SolI | Streptoverticillium olivoverticillatum | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, Bce751I, CelI, OkrAI, SolI, SurI | | Sol10179I | Streptomyces olivochromogenes ST10179 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | | SpaHI | Synechococus parietina | GCATGC | 5 | | | SpeI | Sphaerotilus natans | ACTAGT | 1 | AhII, AclNI, BcuI | | SphI | Streptomyces phaeochromogenes | GCATGC | 5 | | | SplI | Spirulina platensis | CGTACG | 1 | | | SpmI | Sphingobacterium multivorum RFL21 | ATCGAT | 2 | BanIII, BbvAII, BdiI, BscI, Bsa29I, BspJI, ClaI, LcaI, PgaI, Ssp27144I | | SpoI | Salmonella potsdam | TCGCGA | 3 | | | SpuI | Streptomyces pulveraceus | CCGCGG | 4 | | | SrfI | Streptomyces sp. | GCCCGGGC | 4 | | | SrlI | Selenomonas ruminantium lactilytica 84 | GCCGGC | 1 | | | Srl5DI | Selenomonas ruminantium 5 | CTGCAG | 5 | AliAJI, Asp713I, BspMAI, BsuBI, CfrA4I, Pfl21I, PstI, SflI, Srl5DI | | Srl32DII | Selenomonas ruminantium 32 | GAATTC | 1 | | | Srl55DI | Selenomonas ruminantium lactilytica 55 | GAATTC | 1 | | | Srl56DI | Selenomonas ruminantium 56 | CTRYAG | 1 | | | SruI | Selenomonas ruminantium 18D | TTTAAA | 3 | AhaIII, DraI, PauAII | | Sru4DI | Selenomonas ruminantium | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, VspI | | Sru30DI | Selenomonas ruminantium 30 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, SseBI, SteI, StuI | | SsbI | Streptomyces scabies | AAGCTT | 1 | | | SscL1I | Staphylococcus sp. L1 | GANTC | 1 | | | Sse9I | Sporosarcina sp. 9 | AATT | 1 | | | Sse232I | Streptomyces sp. RH232 | CGCCGGCG | 2 | | | Sse1825I | Streptomyces sp. | GGGWCCC | 2 | | | Sse8387I | Streptomyces sp. 8387 | CCTGCAGG | 6 | | | Sse8647I | Streptomyces sp. | AGGWCCT | 2 | | | SseAI | Streptomyces sp. | GGCGCC | 2 | | | SseBI | Streptomyces sp. | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SteI, StuI | | SshAI | Salmonella shikmonah | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | SsiI | Staphylococcus sciuri RFL1 | CCGC | 1 | AciI | | SsiAI | Staphylococcus sp. A | GATC | 1 | BscFI, BspAI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | | SsiBI | Staphylococcus sp. B | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | | SslI | Streptococcus salivarius thermophilus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, MvaI | | SsoI | Shigella sonnei 47 | GAATTC | 1 | | | SsoII | Shigella sonnei 47 | CCNGG | 1 | | | SspI | Sphaerotilus sp. | AATATT | 3 | | | Ssp1I | Streptomyces sp. RFL1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PlaII, SfuI, SspRFI, SviI | | Ssp4800I | Streptomyces sp. BMTU 4800 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, SspBI | | Ssp5230I | Streptomyces sp. 5230 | GACGTC | 5 | AatII, ZraI | | Ssp27144I | Synechococcus sp. | ATCGAT | 2 | BanIII, BavCI, BbvAII, BscI, BspJI, BspOVII, BstNZ169I, ClaI, LcaI | | SspAI | Synechococcus sp. | CCWGG | 1 | AeuI, AorI, Bse17I, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | | SspBI | Streptomyces sp. | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, Ssp4800I | | SspCI | Streptomyces sp. | GCCGGC | 3 | | | SspD5I | Staphylococcus sp. D5 | GGTGA | 8 | AsuHPI, HphI | | SspD5II | Staphylococcus sp. D5 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SepI, Zsp2I | | SspRFI | Synechococcus sp. RF-1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I, SviI | | SsrI | Staphylococcus saprophyticus B6 | GTTAAC | 3 | | | SstI | Streptomyces stanford | GAGCTC | 5 | | | SstII | Streptomyces stanford | CCGCGG | 4 | | | Sst12I | Streptomyces sp. ST-12 | CTGCAG | 5 | Asp713I, BloHII, BspMAI, BsuBI, CfuII, Psp23I, PstI, SflI, Srl5DI | | SteI | Streptomyces tendae | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, StuI | | SthI | Salmonella thompson YY356 | GGTACC | 1 | Acc65I, AhaB8I, Asp718I, KpnI, | | Sth117I | Streptococcus thermophilus ST117 | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, EcoRII, MvaI, SspAI | | Sth132I | Streptococcus thermophilus | CCCG | 8 | | | Sth134I | Streptococcus thermophilus 134 | CCGG | 1 | | | Sth368I | Streptococcus thermophilus CNRZ368 | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | | StrI | Streptomyces thermodiastaticus | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | | StsI | Streptococcus sanguis 54 | GGATG | 9 | | | StuI | Streptomyces tubercidicus | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI | | StyI | Salmonella typhi | CCWWGG | 1 | | | StyD4I | Salmonella typhi D4 | CCNGG | 1 | | | SuaI | Sulfolobus acidocaldarius | GGCC | 2 | | | SuiI | Sulfolobus islandicus REN2HI | GCWGC | 1 | AceI, ApeKI, Taq52I, TseI | | SunI | Synechococcus uniformis | CGTACG | 1 | | | SurI | Sporosarcina ureae 2 | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, OkrAI, RspLKII, SolI | | SviI | Streptomyces violochromogenes | TTCGAA | 2 | AsuII, Bpu14I, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I | | SwaI | Staphylococcus warneri | ATTTAAAT | 4 | |","Markdown" "Bioengineering","telatin/seqfu2","re/Bst-Bv.md",".md","17071","106","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:----------|:------------------------------------|:-----------------------|------:|:--------------------------------------------------------------------------| | BstI | Bacillus stearothermophilus 1503-4R | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, Nsp29132II | | Bst1I | Bacillus stearothermophilus 1 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | | Bst2I | Bacillus stearothermophilus 2 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, BstOI, Bst2UI, CthII, EcoRII, MvaI | | Bst6I | Bacillus stearothermophilus 6 | CTCTTC | 7 | | | Bst11I | Bacillus stearothermophilus 11 | ACTGG | 6 | | | Bst12I | Bacillus stearothermophilus 12 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst71I, BstV1I | | Bst19I | Bacillus stearothermophilus 19 | GCATC | 9 | | | Bst19II | Bacillus stearothermophilus 19 | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | | Bst28I | Bacillus stearothermophilus 28 | ATCGAT | 2 | BciBI, BdiI, Bli41I, Bsa29I, Bsp106I, BspDI, LplI, SpmI, ZhoI | | Bst38I | Bacillus stearothermophilus 38 | CCWGG | 2 | AorI, BseBI, Bse17I, BsiLI, BspNI, BstOI, Bst2UI, EcoRII, MvaI | | Bst40I | Bacillus stearothermophilus 40 | CCGG | 1 | | | Bst71I | Bacillus stearothermophilus 71 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, BstV1I | | Bst98I | Bacillus stearothermophilus C98 | CTTAAG | 1 | | | Bst100I | Bacillus stearothermophilus 100 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | | Bst1107I | Bacillus stearothermophilus RFL1107 | GTATAC | 3 | | | BstACI | Bacillus stearothermophilus AC | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, HgiDI, Hsp92I | | BstAUI | Bacillus stearothermophilus AU | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, Ssp4800I, SspBI | | BstBI | Bacillus stearothermophilus B225 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, LspI, NspV, SspRFI | | Bst2BI | Bacillus stearothermophilus 2B | CACGAG | 1 | | | BstBAI | Bacillus stearothermophilus BA | YACGTR | 3 | | | BstBSI | Bacillus stearothermophilus BS | GTATAC | 3 | | | BstB7SI | Bacillus stearothermophilus B7S | RCCGGY | 1 | | | BstBS32I | Bacillus stearothermophilus BS32 | GAAGAC | 8 | | | BstBZ153I | Bacillus stearothermophilus BZ153 | GCGCGC | 1 | | | Bst4CI | Bacillus stearothermophilus 4C | ACNGT | 3 | | | BstC8I | Bacillus stearothermophilus C8 | GCNNGC | 3 | | | BstD102I | Bacillus stearothermophilus D102 | CCGCTC | 3 | AccBSI, BsrBI, Bst31NI, MbiI | | BstDEI | Bacillus stearothermophilus DE | CTNAG | 1 | | | BstDSI | Bacillus stearothermophilus DS | CCRYGG | 1 | | | BstEII | Bacillus stearothermophilus ET | GGTNACC | 1 | AcrII, BstPI, BstT9I, BstT10I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | | BstENII | Bacillus stearothermophilus EN | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | | BstEZ359I | Bacillus stearothermophilus EZ359 | GTTAAC | 3 | | | BstFI | Bacillus stearothermophilus FH58 | AAGCTT | 1 | | | BstF5I | Bacillus stearothermophilus F5 | GGATG | 7 | | | BstFNI | Bacillus stearothermophilus | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BstUI, Csp68KVI, FauBII, MvnI, SelI | | BstFZ438I | Bacillus stearothermophilus FZ438 | CCCGC | 9 | | | BstGZ53I | Bacillus stearothermophilus GZ53 | CGTCTC | 7 | | | BstH2I | Bacillus stearothermophilus H2 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, HaeII, LpnI | | BstH9I | Bacillus stearothermophilus H9 | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI,  Bst31TI, BthII, Bth617I, EacI | | BstHHI | Bacillus stearothermophilus HH | GCGC | 3 | AspLEI, BspLAI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | | BstHPI | Bacillus stearothermophilus HP | GTTAAC | 3 | | | BstIZ316I | Bacillus stearothermophilus IZ316 | CACNNNGTG | 6 | AdeI, DraIII | | BstJZ301I | Bacillus stearothermophilus JZ301 | CTNAG | 1 | | | BstKTI | Bacillus stearothermophilus KT | GATC | 3 | AspMDI, Bsp2095I, Bst19II, BspKT6I, DpnII, MboI, NmeCI, SsiAI | | BstM6I | Bacillus stearothermophilus M6 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, Fsp1604I, MvaI | | BstMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BsoMAI | | BstMBI | Bacillus stearothermophilus MB | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I | | BstMCI | Bacillus stearothermophilus MC | CGRYCG | 4 | | | BstMZ611I | Bacillus stearothermophilus MZ611 | CCNGG | 1 | | | BstNI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, Bst2UI, Fsp1604I, SniI, Sth117I | | Bst31NI | Bacillus stearothermophilus 31N | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, MbiI | | BstNSI | Bacillus stearothermophilus 1161NS | RCATGY | 5 | | | BstNZ169I | Bacillus stearothermophilus NZ169 | ATCGAT | 2 | BanIII, BciBI, BdiI, Bli41I, Bsa29I, BspDI, LplI, Rme21I, SpmI, ZhoI | | BstOI | Bacillus stearothermophilus O22 | CCWGG | 2 | AjnI, ApyI, BciBII, BptI, Bst1I, Bst2UI, Fsp1604I, SniI, Sth117I | | BstOZ616I | Bacillus stearothermophilus OZ616 | GGGAC | 9 | | | BstPI | Bacillus stearothermophilus | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT9I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | | BstPZ418I | | GGATG | 8 | | | BstPZ740I | Bacillus stearothermophilus PZ740 | CTTAAG | 1 | | | BstRZ246I | Bacillus stearothermophilus RZ246 | ATTTAAAT | 4 | | | BstSI | Bacillus stearothermophilus S183 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, NspIII, OfoI, PunAI | | BstSCI | Bacillus stearothermophilus SC | CCNGG | 1 | | | BstSFI | Bacillus stearothermophilus SF | CTRYAG | 1 | | | BstSNI | Bacillus stearothermophilus SN | TACGTA | 3 | | | BstSWI | Bacillus stearothermophilus SW | ATTTAAAT | 4 | | | BstT7I | Bacillus stearothermophilus T7 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, FbaI, Ksp22I,  ParI | | BstT9I | Bacillus stearothermophilus T9 | GGTNACC | 1 | AspAI, Bse64I, BstT10I, BstPI, Eco91I, EcoO128I, NspSAII, PspEI | | BstT10I | Bacillus stearothermophilus T10 | GGTNACC | 1 | AspAI, BseT10I, BstEII, BstT10I, Eco91I, EcoO128I, NspSAII, PspEI | | Bst31TI | Bacillus stearothermophilus 31T | GGATC | 9 | | | BstTS5I | Bacillus stearothermophilus TS5 | GAAGAC | 8 | | | BstUI | Bacillus stearothermophilus U458 | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BtkI, Csp68KVI, FauBII, MvnI, SelI | | Bst2UI | Bacillus stearothermophilus 2U | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, SniI, SslI, TaqXI, ZanI | | BstVI | Bacillus stearothermophilus V | CTCGAG | 1 | BluI, BssHI, MlaAI, PanI, SauLPII, SciI, SlaI, StrI, XhoI | | BstV1I | Bacillus stearothermophilus V1 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I | | BstV2I | Bacillus stearothermophilus V2 | GAAGAC | 8 | | | BstX2I | Bacillus stearothermophilus X2 | RGATCY | 1 | | | BstYI | Bacillus stearothermophilus Y406 | RGATCY | 1 | | | BstZI | Bacillus stearothermophilus Z130 | CGGCCG | 1 | AaaI, BseX3I, EagI, EclXI, Eco52I, SenPT16I, XmaIII | | BstZ17I | Bacillus stearothermophilus 38M | GTATAC | 3 | | | Bsu6I | Bacillus subtilis 6v1 | CTCTTC | 7 | | | Bsu15I | Bacillus subtilis 15 | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, BsuTUI, ClaI | | Bsu23I | Bacillus subtilis 23 | TCCGGA | 1 | AccIII, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | | Bsu36I | Bacillus subtilis 36 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | | Bsu54I | Bacillus subtilis 54 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | | Bsu1532I | Bacillus subtilis 1532 | CGCG | 2 | BceBI, Bpu95I, Bsp123I, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | | Bsu1854I | Bacillus subtilis 1854 | GRGCYC | 5 | | | BsuBI | Bacillus subtilis | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, HalII, Psp23I, PstI, SalPI, SflI, YenI | | BsuFI | Bacillus subtilis | CCGG | 1 | | | BsuMI | Bacillus subtilis 168 | CTCGAG | 1 | XhoI, BssHI, TliI, PaeR7I, Sfr274I, SlaI, StrI | | BsuRI | Bacillus subtilis R | GGCC | 2 | HaeIII | | BsuTUI | Bacillus subtilis TU | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, ClaI | | BteI | Brochothrix thermosphacter | GGCC | 2 | | | BtgI | Bacillus thermoglucosidasius | CCRYGG | 1 | | | BtgZI | Bacillus thermoglucosidasius | GCGATG | 10 | | | BthAI | Bacillus thuringiensis AII | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | | BthCI | Bacillus thuringiensis 2294 | GCNGC | 4 | | | BthDI | Bacillus thuringiensis D4 | CCWGG | 2 | AorI, ApyI, Bse24I, BstNI, BstOI, Bst2UI, CbrI, EcoRII, MvaI, SleI | | BthEI | Bacillus thuringiensis E | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | | BtkI | Bacillus thuringiensis Kumantoensis | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | | BtkII | Bacillus thuringiensis Kumantoensis | GATC | 1 | BfuCI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NmeCI, SauMI | | BtrI | Bacillus stearothermophilus SE-U62 | CACGTC | 3 | | | BtsI | Bacillus thermoglucosidasius | GCAGTG | 8 | | | BveI | Brevundimonas vesicularis RFL1 | ACCTGC | 10 | Acc36I, BfuAI, BspMI | | BvuI | Bacillus vulgatis | GRGCYC | 5 | | | BvuBI | Bacteroides vulgatus | CGTACG | 1 | |","Markdown" "Bioengineering","telatin/seqfu2","re/O-R.md",".md","20097","124","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:-----------|:--------------------------------------|:-----------------------|------:|:------------------------------------------------------------------------| | OfoI | Oscillatoria foreaui A-1340 | CYCGRG | 1 | AquI, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, PlaAI, PunAI | | OkrAI | Oceanospirillum kriegii | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, BstI, OkrAI, SolI, Uba4009I | | OxaNI | Oerskovia xanthineolytica N | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | PabI | Pyrococcus abyssi | GTAC | 3 | AfaI, Csp6I, CviQI, HpyBI, HpyBI, PlaAII, RsaI,  RsaNI, | | PacI | Pseudomonas alcaligenes | TTAATTAA | 5 | | | Pac25I | Pseudomonas alcaligenes | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PspAI, PspALI, XcyI, XmaI, XmaCI | | PaeI | Pseudomonas aeruginosa | GCATGC | 5 | | | PaeAI | Pseudomonas aeruginosa | CCGCGG | 4 | | | PaeBI | Pseudomonas aeruginosa - 18 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | | PaeHI | Pseudomonas aeruginosa 4148 | GRGCYC | 5 | | | PaeHII | Pseudomonas aeruginosa 4148 | CTGCAG | 5 | AliAJI, BspBI, BspMAI, CfuII, Ecl2zI, HalII, Srl5DI, Sst12I, XcpI | | PaeQI | Pseudomonas aeruginosa Q2 | CCGCGG | 4 | | | PaeR7I | Pseudomonas aeruginosa PA0303 pMG7 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | | Pae2kI | Pseudomonas aeruginosa 2k | AGATCT | 1 | | | Pae5kI | Pseudomonas aeruginosa 5k | CCGCGG | 4 | | | Pae14kI | Pseudomonas aeruginosa 14k | CCGCGG | 4 | | | Pae17kI | Pseudomonas aeruginosa 17k | CAGCTG | 3 | | | Pae18kI | Pseudomonas aeruginosa 18k | AGATCT | 1 | | | PagI | Pseudomonas alcaligenes Sau 14-027 | TCATGA | 1 | | | PalI | Providencia alcalifaciens | GGCC | 2 | | | PamI | Phormidium ambiguum | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, Pun14627I | | PamII | Phormidium ambiguum | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiDI, HgiGI, HgiHII, Hin1I, Hsp92I, Msp17I | | PanI | Pseudomonas alkanolytica | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | | PasI | Pseudomonas anguilliseptica RFL1 | CCCWGGG | 2 | — None on May 2010 — | | PauI | Paracoccus alcaliphilus ZVK3-3 | GCGCGC | 1 | | | PauAI | Phormidium autumnale | RCATGY | 5 | | | PauAII | Phormidium autumnale | TTTAAA | 3 | AhaIII, DraI, SruI | | PceI | Planococcus citreus 55 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | | PciI | Planococcus citreus SE-F45 | ACATGT | 1 | | | PctI | Planococcus citreus SM | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI BmaHI, BsaMI, BscCI, Mva1269I | | Pde12I | Paracoccus denitrificans 12 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | | Pde133I | Paracoccus denitrificans 133 | GGCC | 2 | | | Pde137I | Paracoccus denitrificans 137 | CCGG | 1 | | | PdiI | Pseudomonas diminuta Mck 33-321 | GCCGGC | 3 | | | PfaAI | Phormidium favosum | GGYRCC | 1 | AccB1I, BanI, BbvBI, BshNI, Eco64I, HgiCI, HgiHI, MspB4I | | PfaAII | Phormidium favosum | CATATG | 2 | | | PfaAIII | Phormidium favosum | GCATGC | 5 | | | PfeI | Psychrobacter faecalis RFL1 | GAWTC | 1 | | | Pfl8I | Pseudomonas fluorescens 8 | GGATCC | 1 | AliAJI, BspBI, BsuBI, CflI, CfrA4I, PaePI, Pfl21I, PstI, SflII, Sst12I | | Pfl21I | Pseudomonas sp. 21 | CTGCAG | 5 | | | Pfl23II | Pseudomonas fluorescens RFL23 | CGTACG | 1 | | | Pfl27I | Pseudomonas fluorescens RFL27 | RGGWCCY | 2 | | | PflFI | Pseudomonas fluorescens biotype F | GACNNNGTC | 4 | AspI, AtsI, PsyI, TelI, Tth111I | | PflKI | Pseudomonas fluorescens | GGCC | 2 | | | PfoI | Pseudomonas fluorescens biovar 126 | TCCNGGA | 1 | | | PgaI | Pseudomonas gladioli B4 | ATCGAT | 2 | BanIII, BbvAII, BliAI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | | PhaI | Pasteurella haemolytica | GCATC | 8 | | | PhoI | Pyrococcus horikoshii OT3 | GGCC | 2 | | | PinAI | Pseudomonas inequalis | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, CspAI | | PinBI | Phormidium inundatum | ATGCAT | 5 | EcoT22I, BfrBI, Mph1103I, NsiI, Ppu10I, SepI, SspD5II, Zsp2I | | PinBII | Phormidium inundatum | TCCGGA | 1 | Aor13HI, BlfI, Bsp13I, BspEI, Bsu23I, Kpn2I, PinBII, PtaI | | PlaI | Phormidium lapideum | GGCC | 2 | | | PlaII | Phormidium lapideum | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, SfuI, SspRFI | | PlaAI | Phormidium laminosum | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | | PlaAII | Phormidium laminosum | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, RsaI,  RsaNI, | | PleI | Pseudomonas lemoignei | GAGTC | 9 | | | Ple19I | Pseudomonas lemoignei 19 | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, MvrI, Psu161I, PvuI, RshI, XorII | | PmaCI | Pseudomonas maltophilia CB50P | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmlI, PspCI | | PmeI | Pseudomonas mendocina | GTTTAAAC | 4 | MssI | | Pme55I | Pseudomonas mendocina 55 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI, StuI | | PmlI | Pseudomonas maltophilia | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PspCI | | PovII | Proteus vulgaris | CAGCTG | 3 | | | PpaAI | Phormidium papyraceum | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, SfuI, SspRFI, SviI | | PpaAII | Phormidium papyraceum | TCGA | 1 | | | PpeI | Phormidium persicinum | GGGCCC | 5 | ApaI, Bsp120I, PspOMI | | PpsI | Pseudomonas pseudoalcaligenes PL | GAGTC | 9 | | | Ppu10I | Pseudomonas putida RFL10 | ATGCAT | 1 | BfrBI, Csp68KII, EcoT22I, Mph1103I, NsiI, SepI, SspD5II | | Ppu111I | Pseudomonas putida P111 | GAATTC | 1 | | | PpuAI | Pseudomonas putida A1 | CGTACG | 1 | | | PpuMI | Pseudomonas putida M | RGGWCCY | 2 | | | PpuXI | Pseudomonas putida X | RGGWCCY | 2 | | | PshBI | Plesiomonas shigelloides TPS970 | ATTAAT | 2 | AseI, AsnI, BpoAI, Sru4DI, VspI | | PsiI | Pseudomonas sp. SE-G49 | TTATAA | 3 | | | Psp03I | Phormidium sp. | GGWCC | 4 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11AI | | Psp5II | Pseudomonas sp. RFL5 | RGGWCCY | 2 | | | Psp6I | Pseudomonas sp. B6 | CCWGG | 1 | AeuI, AglI, ApaORI, Bse17I, EcoRII, Fsp1604I, SspAI, Sth117I | | Psp23I | Pseudomonas sp. 23 | CTGCAG | 5 | ApiI, BspBI, CflI, MhaAI, Pfl21I, PstI, SalPI, Sst12I, YenI | | Psp1406I | Pseudomonas pseudoalcaligenes RFL1406 | AACGTT | 2 | AclI | | PspAI | Pseudomonas sp. | CCCGGG | 1 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI, XmaCI | | PspALI | Pseudomonas sp. AL1637 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | | Psp124BI | Pseudomonas sp. 124B | GAGCTC | 5 | | | PspCI | Pseudomonas sp. C | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PmlI | | PspEI | Pseudomonas sp. E | GGTNACC | 1 | AcrII, AspAI, BstEII, BstPI, Eci125I, Eco91I, EcoO65I, EcoO128I | | PspGI | Pyrococcus sp. GI-H | CCWGG | 1 | AeuI, AjnI, AorI, Bse17I, EcoRII, Fsp1604I, Psp6I, SspAI, Sth117I | | PspLI | Pseudomonas sp. L | CGTACG | 1 | | | PspN4I | Pseudomonas sp. N4 | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, NlaIV | | PspOMI | Pseudomonas sp. OM2164 | GGGCCC | 1 | ApaI, Bsp120I, PpeI | | PspPI | Psychrobacter immobilis TA137 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | | PspPPI | Pseudomonas sp. PP | RGGWCCY | 2 | | | PspXI | Pseudomonas sp. A1-1 | VCTCGAGB | 2 | | | PssI | Pseudomonas sp. | RGGNCCY | 5 | | | PstI | Providencia stuartii 164 | CTGCAG | 5 | AliAJI, BspBI, CfuII, Ecl2zI, HalII, PstI, Sag16I, Sag23I, Sst12I, XcpI | | PstNHI | Pseudomonas stutzeri NH | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, LlaG2I | | PsuI | Pseudomonas stutzeri Mck 28-pH52 | RGATCY | 1 | | | Psu161I | Pseudomonas stutzeri 161 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, PvuI, RshI, XorII | | PsuAI | Phormidium subfuscum | YACGTR | 3 | | | PsyI | Pseudomonas syringae Lki 1-pH124 | GACNNNGTC | 4 | AspI, AtsI, PflFI, TelI, Tth111I | | PtaI | Phormidium tadzschicicum | TCCGGA | 1 | Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Kpn2I, PinBII, PtaI | | Pun14627I | Phormidium uncinatum 1462/7 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, PamI | | Pun14627II | Phormidium uncinatum 1462/7 | CAGCTG | 3 | | | PunAI | Phormidium uncinatum | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco27kI, Nli3877I, PlaAI | | PunAII | Phormidium uncinatum | RCATGY | 5 | | | PvuI | Proteus vulgaris | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, NblI, Ple19I, Psu161I, RshI, XorII | | PvuII | Proteus vulgaris | CAGCTG | 3 | | | Pvu84II | Proteus vulgaris 84 | CAGCTG | 3 | | | RalF40I | Ruminococcus albus F-40 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, HacI, MkrAI, Sau3AI, SsiAI | | RcaI | Rhodococcus capsulatum | TCATGA | 1 | | | RflFI | Ruminococcus flavefaciens FD-1 | GTCGAC | 1 | | | RflFII | Ruminococcus flavefaciens FD-1 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, ScaI, ZrmI | | RleAI | Rhizobium leguminosarum | CCCACA | 12 | | | RmaI | Rhodothermus marinus | CTAG | 1 | | | Rme21I | Rhizobium meliloti | ATCGAT | 2 | BanIII, BbvAII, BliRI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | | RsaI | Rhodopseudomonas sphaeroides | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, PlaAII,  RsaNI, | | RshI | Rhodopseudomonas sphaeroides 2.4.1 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, Psu161I, PvuI, XorII | | RspLKI | Rhodococcus sp. LK2 | GCATGC | 5 | | | RspLKII | Rhodococcus sp. LK2 | GGATCC | 1 | AliI, AsiI, BamHI, Bce751I, Nsp29132II, OkrAI, RspLKII, SolI | | RspXI | Rhodococcus sp. | TCATGA | 1 | | | RsrI | Rhodopseudomonas sphaeroides | GAATTC | 1 | | | RsrII | Rhodopseudomonas sphaeroides | CGGWCCG | 2 | | | Rsr2I | Rhodobacter sphaeroides SE-I2 | CGGWCCG | 2 | | | RtrI | Rhizobium trifolii | GTCGAC | 1 | | | Rtr63I | Rhizobium trifolii 63 | GTCGAC | 1 | |","Markdown" "Bioengineering","telatin/seqfu2","re/G-K.md",".md","13074","86","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:----------|:-------------------------------|:-----------------------|------:|:----------------------------------------------------------------------| | GalI | Gluconobacter albidus | CCGCGG | 4 | | | GceI | Gluconobacter cerinus | CCGCGG | 4 | | | GceGLI | Gluconobacter cerinus | CCGCGG | 4 | | | GdiI | Gluconobacter dioxyacetonicus | AGGCCT | 3 | AatI, AspMI, Eco147I, PceI, SarI, Sru30DI, SseBI, SteI, StuI | | GdiII | Gluconobacter dioxyacetonicus | CGGCCR | 1 | | | GstI | Geobacillus stearothermophilus | GGATCC | 1 | | | GsuI | Gluconobacter suboxydans H-15T | CTGGAG | 13 | | | HacI | Halococcus acetoinfaciens | GATC | 1 | Bme12I, Bsp67I, BstENII, CcyI, FnuEI, MgoI, NphI, Sau3AI | | HaeI | Haemophilus aegyptius | WGGCCW | 3 | | | HaeII | Haemophilus aegypticus | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, LpnI | | HaeIII | Haemophilus aegypticus | GGCC | 2 | BsuRI | | HalI | Hafnia alvei B6 | GAATTC | 1 | | | HalII | Hafnia alvei B6 | CTGCAG | 5 | AjoI, AliAJI, Bsp63I, CfrA4I, CfuII, CstI, PstI, SflI, Srl5DI, Sst12I | | HapII | Haemophilus aphrophilus | CCGG | 1 | | | HgaI | Haemophilus gallinarum | GACGC | 8 | | | HgiI | Herpetosiphon giganteus 3303 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiHII, Hin1I, PamII | | HgiAI | Herpetosiphon giganteus HP1023 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI,  Bsm6I, HpyF46II, MspV281I | | HgiBI | Herpetosiphon giganteus Hpg5 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Psp03I, VpaK11AI | | HgiCI | Herpetosiphon giganteus Hpg9 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiHI, MspB4I, PfaAI | | HgiCII | Herpetosiphon giganteus Hpg9 | GGWCC | 1 | Bme18I, BthAI, DsaIV, FspMSI, HgiHIII, Psp03I, VpaK11AI | | HgiCIII | Herpetosiphon giganteus Hpg9 | GTCGAC | 1 | | | HgiDI | Herpetosiphon giganteus Hpa2 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiI, Hin1I, PamII | | HgiDII | Herpetosiphon giganteus Hpa2 | GTCGAC | 1 | | | HgiEI | Herpetosiphon giganteus Hpg24 | GGWCC | 1 | Bme216I, BthAI, DsaIV, ErpI, FspMSI, HgiHIII, VpaK11AI | | HgiGI | Herpetosiphon giganteus Hpa1 | GRCGYC | 2 | AcyI, AosII, BbiII, BstACI, HgiI, HgiGI, Msp17I, PamII | | HgiHI | Herpetosiphon giganteus HP1049 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiCI, MspB4I, PfaAI | | HgiHII | Herpetosiphon giganteus HP1049 | GRCGYC | 2 | AosII, AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Msp17I, PamII | | HgiHIII | Herpetosiphon giganteus HP1049 | GGWCC | 1 | Bme216I, DsaIV, ErpI, HgiBI, Psp03I, VpaK11AI, VpaK11BI | | HgiJI | Herpetosiphon giganteus HFS101 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI | | HgiJII | Herpetosiphon giganteus HFS101 | GRGCYC | 5 | | | HgiS22I | Herpetosiphon giganteus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, CauII, Eco1831I, EcoHI, Kpn49kII | | HhaI | Haemophilus haemolyticus | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, SciNI | | HhaII | Haemophilus haemolyticus | GANTC | 1 | | | Hin1I | Haemophilus influenzae RFL1 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, HgiI, HgiDI, HgiDI, Hsp92I | | Hin1II | Haemophilus influenzae RFL1 | CATG | 4 | | | Hin2I | Haemophilus influenzae RFL2 | CCGG | 1 | | | Hin6I | Haemophilus influenzae RFL6 | GCGC | 1 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, HhaI, HsoI, HspAI, SciNI | | HinJCI | Haemophilus influenzae JC9 | GTYRAC | 3 | | | HinP1I | Haemophilus influenzae P1 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HsoI, HspAI, SciNI | | HincII | Haemophilus influenzae Rc | GTYRAC | 3 | | | HindII | Haemophilus influenzae Rd | GTYRAC | 3 | | | HindIII | Haemophilus influenzae Rd | AAGCTT | 1 | | | HinfI | Haemophilus influenzae Rf | GANTC | 1 | | | HjaI | Hyphomonas jannaschiana | GATATC | 3 | | | HpaI | Haemophilus parainfluenzae | GTTAAC | 3 | | | HpaII | Haemophilus parainfluenzae | CCGG | 1 | | | HphI | Haemophilus parahaemolyticus | GGTGA | 9 | AsuHPI, SspD5I | | Hpy8I | Helicobacter pylori A 8-5 | GTNNAC | 3 | | | Hpy51I | Helicobacter pylori 51 | GTSAC | 1 | | | Hpy99I | Helicobacter pylori J99 | CGWCG | 5 | | | Hpy178III | Helicobacter pylori J178 | TCNNGA | 2 | | | Hpy188I | Helicobacter pylori J188 | TCNGA | 3 | | | Hpy188III | Helicobacter pylori J188 | TCNNGA | 2 | | | HpyAV | Helicobacter pylori 26695 | CCTTC | 9 | | | HpyBI | Helicobacter pylori Roberts | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, PabI, PlaAII, RsaI, RsaNI | | HpyBII | Helicobacter pylori Roberts | GTNNAC | 3 | | | HpyCI | Helicobacter pylori | GATATC | 3 | | | HpyC1I | Helicobacter pylori | CCATC | 9 | | | HpyCH4I | Helicobacter pylori CH4 | CATG | 4 | | | HpyCH4III | Helicobacter pylori CH4 | ACNGT | 3 | | | HpyCH4IV | Helicobacter pylori CH4 | ACGT | 1 | | | HpyCH4V | Helicobacter pylori CH4 | TGCA | 2 | | | HpyF44III | Helicobacter pylori RFL44 | TGCA | 2 | | | HsoI | Haemophilus somnus 2336 | GCGC | 1 | AspLEI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, HspAI, SciNI | | Hsp92I | Haemophilus sp. 92 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, HgiI, HgiDI, HgiHII, Hin1I, Hsp92I | | Hsp92II | Haemophilus sp. 92 | CATG | 4 | | | HspAI | Haemophilus sp. A | GCGC | 1 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, SciNI | | HsuI | Haemophilus suis | AAGCTT | 1 | | | ItaI | Ilyobcater tartaricus | GCNGC | 2 | | | KasI | Kluyvera ascorbata | GGCGCC | 1 | | | Kaz48kI | Klebsiella azeanae | RGGNCCY | 5 | | | KoxII | Klebsiella oxytoca | GRGCYC | 5 | | | KpnI | Klebsiella pneumoniae OK8 | GGTACC | 5 | Acc65I, AhaB8I, Asp718I, SthI | | Kpn2I | Klebsiella pneumoniae RFL2 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | | Kpn378I | Klebsiella pneumoniae 378 | CCGCGG | 4 | | | Kpn2kI | Klebsiella pneumoniae 2k | CCNGG | 1 | | | Kpn49kI | Klebsiella pneumoniae 49k | GAATTC | 1 | | | Kpn49kII | Klebsiella pneumoniae 49k | CCSGG | 1 | AhaI, AsuC2I, BcnI, CauII, EcoHI, HgiS22I, Mgl14481I, NciI, | | KspI | Kluyvera sp. | CCGCGG | 4 | | | Ksp22I | Kurthia sp. 22 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, FbaI,  ParI | | Ksp632I | Kluyvera sp. 632 | CTCTTC | 7 | | | KspAI | Kurthia sp. N88 | GTTAAC | 3 | | | Kzo9I | Kurthia zopfii 9 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstMBI, CpfI, LlaAI, NdeII, Sth368I | | Kzo49I | Kurthia zopfii 49 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI |","Markdown" "Bioengineering","telatin/seqfu2","re/Bsp-Bss.md",".md","15588","98","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:-----------|:------------------------------------|:-----------------------|------:|:-----------------------------------------------------------------------| | Bsp6I | Bacillus sp. RFL6 | GCNGC | 2 | | | Bsp13I | Bacillus sp. 13 | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | | Bsp19I | Bacillus sp. 19 | CCATGG | 1 | | | Bsp50I | Bacillus sp. RFL50 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | | Bsp63I | Bacillus sphaericus 63 | CTGCAG | 5 | AjoI, Asp713I, BloHII, MhaAI, Pfl21I, PstI, SalPI, SflI, Sst12I, YenI | | Bsp67I | Bacillus sphaericus 67 | GATC | 1 | AspMDI, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp68I | Bacillus sp. RFL68 | TCGCGA | 3 | NruI | | Bsp98I | Bacillus sp. RFL98 | GGATCC | 1 | AccEBI, AliI, BamHI, BnaI, BstI, CelI, OkrAI, NspSAIV, Pfl8I, SurI | | Bsp105I | Bacillus sphaericus 105 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp106I | Bacillus sphaericus 106 | ATCGAT | 2 | BbvAII, Bci29I, BciBI, BcmI, BspOVII, BstNZ169I, Rme21I | | Bsp119I | Bacillus sp. RFL119 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, FspII, NspV, SspRFI | | Bsp120I | Bacillus sp. RFL120 | GGGCCC | 1 | ApaI, PpeI, PspOMI | | Bsp123I | Bacillus sp. 123 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | | Bsp143I | Bacillus sp. RFL143 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I, Sau3AI | | Bsp143II | Bacillus sp. RFL143 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, BstH2I, HaeII, LpnI | | Bsp211I | Bacillus sphaericus 211 | GGCC | 2 | | | Bsp423I | Bacillus sp. 423 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bst12I, Bst71I, BstV1I | | Bsp519I | Bacillus sp. 519 | GRGCYC | 5 | | | Bsp1286I | Bacillus sphaericus | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, NspII, SduI | | Bsp1407I | Bacillus stearothermophilus RFL1407 | TGTACA | 1 | AauI,  BsmRI, BsrGI, BstAUI, Ssp4800I, SspBI | | Bsp1720I | Bacillus sp. 1720 | GCTNAGC | 2 | | | Bsp1894I | Bacillus sphaericus 1894 | GGNCC | 1 | AspS9I, Bac36I, BavBII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | | Bsp2095I | Bacillus sphaericus 2095 | GATC | 1 | Bfi57I, Bsp143I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | Bsp4009I | Bacillus sp. 4009 | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, BstI, CelI, OkrAI, Pfl8I, RspLKII, SurI | | BspAI | Bacillus sphaericus JL4B | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | BspA2I | Bacillus sp. A2 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, XmaJI | | Bsp153AI | Bacillus sp. 153A | CAGCTG | 3 | | | BspAAI | Bacillus sp. AA | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | | BspAAII | Bacillus sp. AA | TCTAGA | 1 | | | BspAAIII | Bacillus sp. AA | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, Pfl8I, RspLKII, SolI | | BspANI | Bacillus sp. AN | GGCC | 2 | | | BspBI | Bacillus sphaericus JL14 | CTGCAG | 5 | AjoI, ApiI, Asp713I, BloHII, CfrA4I, Pfl21I, PstI, SalPI, Sst12I, YenI | | BspBII | Bacillus sphaericus JL14 | GGNCC | 1 | AsuI, Bac36I, BavBII, BshKI, BspF4I, CcuI, MaeK81II, PspPI | | BspBRI | Bacillus sp. | GGCC | 2 | | | BspBS31I | Bacillus sp. BS31 | GAAGAC | 8 | | | BspCI | Bacillus sp. C1 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, ErhB9I, NblI, Psu161I, RshI, XorII | | BspCNI | Bacillus sp. 1310 | CTCAG | 10 | | | BspDI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, Bsu15I, BsuTUI, ClaI, ZhoI | | BspD6I | Bacillus sp. D6 | GACTC | 9 | | | BspEI | Bacillus sp. | TCCGGA | 1 | AccIII, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, MroI, PinBII | | BspFI | Bacillus sp. | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | | BspF4I | Bacillus sp. F4 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | | BspHI | Bacillus sp. H3 | TCATGA | 1 | | | BspIS4I | Bacillus sp. IS4 | GAAGAC | 8 | | | BspJI | Bacillus sp. | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NmeCI, SsiAI | | BspJII | Bacillus sp. | ATCGAT | 2 | Bsa29I, BseCI, Bsp106I, BspDI, BspOVII, BspXI, BspZEI | | BspKI | Bacillus sp. K | GGCC | 2 | | | BspKT5I | Bacillus sp. | CTGAAG | 13 | | | BspKT6I | Bacillus sp. KT6 | GATC | 3 | BfuCI, Bsp2095I, Bst19II, BstKTI, DpnII, LlaAI, NmeCI, SsiAI | | BspKT8I | Bacillus sp. KT8 | AAGCTT | 1 | | | BspLI | Bacillus sp. RJ3-212 | GGNNCC | 3 | AspNI, BscBI,  BmiI, NlaIV, PspN4I | | BspLAI | Bacillus sp. LA | GCGC | 3 | AspLEI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | | BspLAII | Bacillus sp. LA | TTCGAA | 2 | | | BspLAIII | Bacillus sp. LA | AAGCTT | 1 | | | BspLS2I | Bacillus sp. LS2 | GDGCHC | 5 | AocII, BmyI, BsoCI, BspLS2I, MhlI, NspII, SduI | | BspLU4I | Bacillus sp. LU4 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, NspSAI, OfoI | | BspLU11I | Bacillus sp. LU11 | ACATGT | 1 | | | BspLU11III | Bacillus sp. LU11 | GGGAC | 9 | | | BspMI | Bacillus sp. M | ACCTGC | 10 | Acc36I, BfuAI, BveI | | BspMII | Bacillus sp. M | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspEI, Bsu23I, CauB3I, MroI | | BspM39I | Bacillus sp. M39 | CAGCTG | 3 | | | BspM90I | Bacillus sp. M90 | GTATAC | 3 | | | BspMAI | Bacillus stearothermophilus MA | CTGCAG | 5 | AjoI, Asp713I, BloHII, PaePI, Psp23I, PstI, SalPI, Sst12I, YenI | | BspMKI | Bacillus sp. MKI | GTCGAC | 1 | | | BspNI | Bacillus sp. N | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | | BspO4I | Bacillus sp. O-4 | CAGCTG | 3 | | | BspOVII | Bacillus sp. OV | ATCGAT | 2 | BanIII, BavCI, BciBI, BcmI, Bli86I, BliRI, BspJII, BstNZ169I, SpmI | | BspPI | Bacillus sp. d 1-34 | GGATC | 9 | AclWI, AlwI, BinI,  BsrWI, BstH9I,  Bst31TI, Bth617I, EacI | | BspRI | Bacillus sphaericus R | GGCC | 2 | | | BspR7I | Bacillus sp. R7 | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | | BspST5I | Bacillus sp. ST5 | GCATC | 8 | | | BspTI | Bacillus sp. RFL1265 | CTTAAG | 1 | AflII | | BspT104I | Bacillus sp. T104 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BstBI, Csp45I, LspI, NspV, SspRFI | | BspT107I | Bacillus sp. T107 | GGYRCC | 1 | AccB1I, BanI, BbvBI, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BspTNI | Bacillus sp. TN | GGTCTC | 7 | | | BspTS514I | Bacillus sp. TS514 | GAAGAC | 8 | | | BspXI | Bacillus sphaericus X | ATCGAT | 2 | BliAI, BliRI, BscI, Bst28I, Bsu15I, LcaI, PgaI, Ssp27144I, ZhoI | | BspXII | Bacillus sphaericus X | TGATCA | 1 | AbaI, BclI, BsiQI, BstT7I, FbaI, Ksp22I,  ParI | | BspZEI | Bacillus sp. ZE | ATCGAT | 2 | Bsa29I, BseCI, BspDI, BspXI, Bst28I, BstNZ169I, BsuTUI, LplI | | BsrI | Bacillus stearothermophilus | ACTGG | 6 | | | BsrAI | Bacillus stearothermophilus CPW7 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | | BsrBI | Bacillus stearothermophilus CPW193 | CCGCTC | 3 | AccBSI, BstD102I, Bst31NI, MbiI | | BsrDI | Bacillus stearothermophilus D70 | GCAATG | 8 | | | BsrFI | Bacillus stearothermophilus CPW16 | RCCGGY | 1 | | | BsrGI | Bacillus stearothermophilus GR75 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BstAUI, Ssp4800I, SspBI | | BsrSI | Bacillus stearothermophilus CPW19 | ACTGG | 6 | | | BssAI | Bacillus sp. | RCCGGY | 1 | | | BssECI | Bacillus stearothermophilus EC | CCNNGG | 1 | | | BssHI | Bacillus stearothermophilus H3 | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | | BssHII | Bacillus stearothermophilus H3 | GCGCGC | 1 | | | BssIMI | Bacillus stearothermophilus IM | GGGTC | 2 | | | BssKI | Bacillus stearothermophilus TBI | CCNGG | 1 | | | BssNAI | Bacillus stearothermophilus NA | GTATAC | 3 | | | BssNI | Bacillus sphaericus KTN | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, Hsp92I, Msp17I | | BssSI | Bacillus stearothermophilus S719 | CACGAG | 1 | | | BssT1I | Bacillus stearothermophilus T1 | CCWWGG | 1 | |","Markdown" "Bioengineering","telatin/seqfu2","re/Bsa-Bso.md",".md","12567","79","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:---------|:---------------------------------------|:-----------------------|------:|:----------------------------------------------------------------------| | BsaI | Bacillus stearothermophilus 20241 | GGTCTC | 7 | Bso31I, BspTNI, Eco31I | | Bsa29I | Bacillus sp. 29 | ATCGAT | 2 | AagI, BanIII, BavCI, BseCI, BspDI, Bsu15I, BsuTUI, ClaI, BbvAII | | BsaAI | Bacillus stearothermophilus G668 | YACGTR | 3 | | | BsaHI | Bacillus stearothermophilus CPW11 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BbiII, BstACI, HgiI, PamII | | BsaJI | Bacillus stearothermophilus J695 | CCNNGG | 1 | | | BsaMI | Bacillus stearothermophilus M293 | GAATGC | 7 | Asp26HI, Asp35HI, Asp36HI, Asp50HI, BsaMI, BsmI, Mva1269I | | BsaOI | Bacillus stearothermophilus O-122 | CGRYCG | 4 | | | BsaWI | Bacillus stearothermophilus W1718 | WCCGGW | 1 | | | BscI | Bacillus sp. | ATCGAT | 2 | BanIII, BavCI, Bci29I, BdiI, Bli41I, BliAI, LplI, PgaI, SpmI | | Bsc91I | Bacillus sp. | GAAGAC | 8 | | | BscAI | Bacillus schlegelii S3 | GCATC | 9 | | | BscBI | Bacillus sp. A11 | GGNNCC | 3 | AspNI,  BmiI, BspLI, NlaIV, PspN4I | | BscCI | Bacillus sp. 2G | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI, Asp36HI, BsaMI, BscCI, PctI | | BscFI | Bacillus sp. JY391 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, CviAI, Kzo9I, NlaII, SsiBI | | Bse1I | Bacillus stearothermophilus 1 | ACTGG | 6 | | | Bse15I | Bacillus sp. 15 | CYCGRG | 1 | Ama87I, AvaI, BcoI, BsoBI, BstSI, Eco88I, NspSAI, OfoI | | Bse16I | Bacillus sp. 16 | CCWGG | 2 | AeuI, BseBI, BsiLI, BstNI, BstM6I, BthDI, BthEI, EcoRII, MvaI | | Bse17I | Bacillus sp. 17 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | | Bse21I | Bacillus sp. 21 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | | Bse24I | Bacillus sp. 24 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | | Bse64I | Bacillus sp. 64 | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BstPI, EcaI, Eci125I, EcoO65I, NspSAII | | Bse118I | Bacillus sp. 118 | RCCGGY | 1 | | | Bse634I | Bacillus sp. 634 | RCCGGY | 1 | | | BseAI | Bacillus sphaericus | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, Kpn2I | | BseBI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, AorI, Bse17I, Bst1I, BstOI, Bst2UI, EcoRII, MvaI, SleI, ZanI | | BseCI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BspDI, Bsu15I, BsuTUI, ClaI, LcaI | | BseDI | Bacillus stearothermophilus RFL1434 | CCNNGG | 1 | | | Bse3DI | Bacillus stearothermophilus 3D | GCAATG | 8 | | | BseGI | Bacillus stearothermophilus Vs 34-031 | GGATG | 7 | | | BseKI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | | BseMI | Bacillus stearothermophilus Isl 15-111 | GCAATG | 8 | | | BseMII | Bacillus stearothermophilus Isl 15-111 | CTCAG | 10 | | | BseNI | Bacillus sp. N | ACTGG | 6 | | | BsePI | Bacillus stearothermophilus P6 | GCGCGC | 1 | | | BseQI | Bacillus sp. Q | GGCC | 2 | | | BseRI | Bacillus sp. R | GAGGAG | 11 | | | BseSI | Bacillus stearothermophilus Jo-553 | GKGCMC | 5 | | | BseT9I | Bacillus sp. T9 | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstT9I, EcaI, Eci125I, EcoO65I, NspSAII, PspEI | | BseT10I | Bacillus sp. T10 | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT10I, BstPI, EcoO128I, EcoO65I, PspEI | | BseXI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseKI, Bsp423I, Bst12I, Bst71I, BstV1I | | BseX3I | Bacillus stearothermophilus X3 | CGGCCG | 1 | AaaI, BstZI, EagI, EclXI, Eco52I, SenPT16I, XmaIII | | BseYI | Bacillus sp. 2521 | CCCAGC | 1 | | | BseZI | Bacillus sp. Z | CTCTTC | 7 | | | BsgI | Bacillus sphaericus B922 | GTGCAG | 13 | | | BshI | Bacillus sphaericus | GGCC | 2 | | | Bsh45I | Bacillus sphaericus 45 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | | Bsh1236I | Bacillus sphaericus RFL1236 | CGCG | 2 | AccII, BceBI, BspFNI, Bsp50I, Csp68KVI, FauBII, MvnI, SelI | | Bsh1285I | Bacillus sphaericus RFL1285 | CGRYCG | 4 | | | BshFI | Bacillus sphaericus | GGCC | 2 | | | BshGI | Bacillus sphaericus | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, PspGI, SspAI | | BshKI | Bacillus sphaericus | GGNCC | 1 | AspS9I, Bac36I, BavAII, Bsp1894I, BspBII, CcuI, MaeK81II, Pde12I | | BshNI | Bacillus sphaericus TK-45 | GGYRCC | 1 | BanI, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | | BshTI | Bacillus sphaericus Jo22-024 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, CsiAI CspAI, PinAI | | BsiI | Bacillus sphaericus | CACGAG | 1 | | | BsiCI | Bacillus sp. | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, Csp45I, FspII, NspV, PpaAI, SfuI | | BsiEI | Bacillus sp. | CGRYCG | 4 | | | BsiHKAI | Bacillus stearothermophilus | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I,  Bsm6I, HgiAI, MspV281I | | BsiHKCI | Bacillus sp. HKC | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | | BsiKI | Bacillus sp. | GGTNACC | 1 | | | BsiLI | Bacillus sp. | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, BstNI, Bst38I, Bst100I, EcoRII, MvaI | | BsiMI | Bacillus sp. | TCCGGA | 1 | AccIII, BbvAIII, BlfI, Bsp13I, BspMII, Bsu23I, Kpn2I, PinBII | | BsiQI | Bacillus sp. | TGATCA | 1 | AbaI, BclI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | | BsiSI | Bacillus sp. | CCGG | 1 | | | BsiWI | Bacillus sp. | CGTACG | 1 | | | BsiXI | Bacillus sp. X | ATCGAT | 2 | BscI, BsiXI, Bsp106I, BspDI, Bsu15I, BsuTUI, ClaI, Rme21I | | BsiZI | Bacillus sp. | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | | BslFI | Bacillus stearothermophilus FI | GGGAC | 9 | | | BsmI | Bacillus stearothermophilus NUB | GAATGC | 7 | Asp26HI, Asp36HI, Asp40HI, BmaHI, BscCI, Mva1269I, PctI | | BsmAI | Bacillus stearothermophilus A664 | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsoMAI, BstMAI | | BsmBI | Bacillus stearothermophilus B61 | CGTCTC | 7 | | | BsmFI | Bacillus stearothermophilus F | GGGAC | 9 | | | BsmSI | Bacillus stearothermophilus CP114 | CCWWGG | 1 | | | Bso31I | Bacillus stearothermophilus E31 | GGTCTC | 7 | | | BsoBI | Bacillus stearothermophilus JN2091 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | | BsoCI | Bacillus stearothermophilus AU891 | GDGCHC | 5 | AocII, BmyI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | | BsoFI | Bacillus stearothermophilus F66 | GCNGC | 2 | | | BsoMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BstMAI |","Markdown" "Bioengineering","telatin/seqfu2","re/Bd-Bp.md",".md","9607","64","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:---------|:--------------------------------|:-----------------------|------:|:--------------------------------------------------------------------| | BdiI | Brevibacterium divaricatum | ATCGAT | 2 | BavCI, Bci29I, Bli41I, Bli86I, BseCI, BsuTUI, Rme21I, SpmI | | BdiSI | Bacteroides distasonis | CTRYAG | 1 | | | BecAII | Brevibacterium sp. A | GGCC | 2 | | | BepI | Brevibacterium epidermidis | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, BtkI, FalII, FauBII, ThaI | | BetI | Brevibacterium acetyliticum | WCCGGW | 1 | | | BfaI | Bacteroides fragilis | CTAG | 1 | | | BfiI | Bacillus firmus S8120 | ACTGGG | 11 | BmrI | | Bfi57I | Butyrivibrio fibrisolvens OB157 | GATC | 1 | Bsp105I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, SsiBI | | Bfi89I | Butyrivibrio fibrisolvens OB189 | YGGCCR | 1 | | | BfmI | Bacillus firmus S8-336 | CTRYAG | 1 | | | BfrI | Bacteroides fragilis | CTTAAG | 1 | | | BfrBI | Bacteroides fragilis BE3 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | | BfuI | Bacillus firmus Auk 22-m21 | GTATCC | 10 | BciVI | | BfuAI | Bacillus fusiformis | ACCTGC | 10 | Acc36I, BspMI, BveI | | BfuCI | Bacillus fusiformis 1226 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, MkrAI, Sth368I | | BglII | Bacillus globigii | AGATCT | 1 | | | BimI | Brevibacterium immotum | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | | Bim19I | Brevibacterium immotum 19 | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | | Bim19II | Brevibacterium immotum 19 | GGCC | 2 | | | BinI | Bifidobacterium infantis 659 | GGATC | 9 | AclWI, AlwI,  BsrWI, BspPI, BstH9I,  Bth617I, EacI | | BlfI | Bacillus licheniformis | TCCGGA | 1 | AccIII, Aor13HI, BseAI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | | Bli41I | Bacillus licheniformis 41 | ATCGAT | 2 | Bci29I, Bli86I, BseCI, BsiXI, BsuTUI, Rme21I, SpmI, Ssp27144I | | Bli86I | Bacillus licheniformis 86 | ATCGAT | 2 | BliAI, Bli41I, BseDI, BsiXI, Rme21I, SpmI, Ssp27144I, ZhoI | | Bli736I | Bacillus licheniformis 736 | GGTCTC | 7 | | | BliAI | Bacillus licheniformis | ATCGAT | 2 | BliRI, Bli41I, BsiXI, BspDI, Rme21I, SpmI, Ssp27144I, ZhoI | | BliHKI | Bacillus licheniformis HK | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | | BliRI | Bacillus licheniformis | ATCGAT | 2 | BciBI, BdiI, Bli41I, BsiXI, BspDI, BspXI, LplI, SpmI, ZhoI | | BlnI | Brevibacterium linens | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BspA2I, XmaJI | | BloHI | Bifidobacterium longum E194b | RGATCY | 1 | | | BloHII | Bifidobacterium longum E194b | CTGCAG | 5 | AjoI, Asp713I, BsuBI, CflI, CfuII, HalII, PstI, SalPI, SflI, Sst12I | | BlpI | Bacillus lentus | GCTNAGC | 2 | | | BluI | Brevibacterium luteum | CTCGAG | 1 | AbrI, BssHI, BstVI, PanI, Sau3239I, Sfr274I, TliI, XhoI | | Bme12I | Bacillus megaterium 12 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, SsiBI | | Bme18I | Bacillus megaterium 18 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI | | Bme142I | Bacillus megaterium 142 | RGCGCY | 3 | AccB2I,  BfoI, Bsp143II, BstH2I, HaeII, LpnI | | Bme216I | Bacillus megaterium 216 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | | Bme361I | Bacillus megaterium 361 | GGCC | 2 | | | Bme585I | Bacillus mesentericus 585 | CCCGC | 9 | | | Bme1390I | Bacillus megaterium RFL1390 | CCNGG | 2 | | | Bme1580I | Bacillus megaterium 1580 | GKGCMC | 5 | | | BmgBI | Bacillus megaterium | CACGTC | 3 | | | BmrI | Bacillus megaterium | ACTGGG | 11 | BfiI | | BmtI | Bacillus megaterium S2 | GCTAGC | 5 | AceII, AsuNHI,  BspOI, NheI, LlaG2I, PstNHI | | BmyI | Bacillus mycoides | GDGCHC | 5 | AocII, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | | BnaI | Bacillus natto B3364 | GGATCC | 1 | AccEBI, BamHI, Bce751I, BstI, CelI, OkrAI, Nsp29132II, Pfl8I, SolI | | BpcI | Bacillus sphaericus | CTRYAG | 1 | | | BpiI | Bacillus pumilus sw 4-3 | GAAGAC | 8 | | | BpmI | Bacillus pumilus | CTGGAG | 12 | | | BpoAI | Bacillus polymyxa | ATTAAT | 2 | AseI, AsnI, PshBI, Sru4DI, VspI | | BptI | Bacillus pantothenticus | CCWGG | 2 | AjnI, BseBI, Bse16I, BstNI, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | | BpuI | Bacillus pumilus AHU1387A | GRGCYC | 5 | | | Bpu10I | Bacillus pumilus 10 | CCTNAGC | 2 | | | Bpu14I | Bacillus pumilus 14 | TTCGAA | 2 | AcpI, AsuII, BsiCI, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | | Bpu95I | Bacillus pumilus 95 | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | | Bpu1102I | Bacillus pumilus RFL1102 | GCTNAGC | 2 | | | BpuAI | Bacillus pumilus | GAAGAC | 8 | | | BpuAmI | Bacillus pumilus | GAGCTC | 3 | | | BpuB5I | Bacillus pumilus | CGTACG | 1 | | | BpuDI | Bacillus pumilus 1117 | CCTNAGC | 2 | | | BpuEI | Bacillus pumilus 2187a | CTTGAG | 12 | | | BpuJI | Bacillus pumilus RFL1458 | CCCGT | 9 | — None on May 2010 — | | BpuSI | Bacillus pumilus | GGGAC | 8 | |","Markdown" "Bioengineering","telatin/seqfu2","re/L-N.md",".md","19163","119","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | |:-----------|:----------------------------------------|:-----------------------|------:|:---------------------------------------------------------------------| | LcaI | Lactobacillus casei | ATCGAT | 2 | BdiI, Bli41I, Bsa29I, BscI, Bsp106I, BspDI, Bst28I, LplI, PgaI, ZhoI | | LlaAI | Lactococcus lactis cremoris W9 | GATC | 1 | Bme12I, Bsp67I, BstENII, ChaI, FnuEI, MgoI, NphI, RalF40I | | LlaBI | Lactococcus lactis cremoris W56 | CTRYAG | 1 | | | LlaCI | Lactococcus lactis W15 | AAGCTT | 1 | | | LlaG2I | Lactococcus lactis cremoris | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, PstNHI | | Lmu60I | Listeria murrayi 60 | CCTNAGG | 2 | AocI, AxyI, BspR7I, CvnI, Lmu60I, MstII, SauI, SshAI | | LplI | Lactobacillus plantarum | ATCGAT | 2 | BanIII, BbvAII, BdiI, Bsa29I, BscI, BstNZ169I, ClaI, LcaI, PgaI | | LpnI | Legionella pneumophila | RGCGCY | 3 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, HaeII | | LspI | Lactobacillus sp. | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp45I, PlaII, PpaAI, Ssp1I | | LweI | Listeria welshimeri RFL131 | GCATC | 8 | | | MabI | Microbacterium arborescens SE | ACCWGGT | 1 | | | MaeI | Methanococcus aeolicus PL-15/H | CTAG | 1 | | | MaeII | Methanococcus aeolicus | ACGT | 1 | | | MaeIII | Methanococcus aeolicus | GTNAC | 1 | | | MaeK81I | Microcystis aeruginosa K-81 | CGTACG | 1 | | | MaeK81II | Microcystis aeruginosa | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | | MavI | Mycobacterium avium | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SciI, SlaI, Sol10179I, XhoI | | MbiI | Moraxella bovis Fr1-022 | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, Bst31NI | | MboI | Moraxella bovis | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | | MboII | Moraxella bovis | GAAGA | 9 | | | MchI | Micromonospora chalcea | GGCGCC | 2 | | | MchAI | Mycobacterium chelonei | GCGGCCGC | 2 | | | MchAII | Mycobacterium chelonei | GGCC | 2 | | | McrI | Micrococcus cryophilus | CGRYCG | 4 | | | MfeI | Mycoplasma fermentans | CAATTG | 1 | | | MflI | Microbacterium flavum | RGATCY | 1 | | | MfoAI | Mycobacterium fortuitum TMC 1529 | GGCC | 2 | | | Mgl14481I | Merismopedia glauca 1448-1 | CCSGG | 2 | AseII, AsuC2I, BcnI, BpuMI, CauII, Eco1831I, EcoHI, HgiS22I, NciI | | MgoI | Mycobacterium gordonae | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, NphI, Sau3AI | | MhaAI | Mycobacterium habana 206 | CTGCAG | 5 | AliAJI, Asp713I, Bsp63I, CstI, Ecl37kI, HalII, PaePI, PstI, YenI | | MhlI | Micrococcus halobius SD | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, SduI | | MkrAI | Micrococcus kristinae | GATC | 1 | Bme12I, BspAI, BstENII, ChaI, FnuEI, MgoI, NphI, Sau3AI | | MlaI | Mastigocladus laminosus | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp68KII, LspI, PlaII, Ssp1I | | MlaAI | Micromonospora lacustris | CTCGAG | 1 | BspAAI, BstVI, PanI, SauLPII, Sbi68I, Sfr274I, SlaI, XhoI | | MlsI | Micrococcus luteus Ng 16-122 | TGGCCA | 3 | | | MltI | Micrococcus luteus | AGCT | 2 | AluBI, AluI | | MluI | Micrococcus luteus | ACGCGT | 1 | | | Mlu23I | Micrococcus luteus 23 | GGATCC | 1 | | | Mlu31I | Micrococcus luteus 31 | TGGCCA | 3 | | | MluB2I | Micrococcus luteus B2 | TCGCGA | 3 | | | MluNI | Micrococcus luteus N | TGGCCA | 3 | | | MlyI | Micrococcus lylae | GAGTC | 8 | | | Mly113I | Micrococcus lylae 113 | GGCGCC | 2 | | | MmeI | Methylophilus methylotrophus | TCCRAC | 12 | | | MnlI | Moraxella nonliquefaciens | CCTC | 9 | | | MnoI | Moraxella nonliquefaciens | CCGG | 1 | | | Mph1103I | Moraxella phenylpyruvica RFL1103 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II | | MroI | Micrococcus roseus | TCCGGA | 1 | BbvAIII, BseAI, Bsp13I, BspEI, Bsu23I, CauB3I, PinBII, PtaI | | MroNI | Micrococcus roseus N | GCCGGC | 1 | | | MscI | Micrococcus sp. | TGGCCA | 3 | | | MseI | Micrococcus sp. | TTAA | 1 | | | MspI | Moraxella sp. | CCGG | 1 | | | Msp17I | Micrococcus sp. 17 | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Hin1I, Msp17I, PamII | | Msp20I | Micrococcus sp. | TGGCCA | 3 | | | Msp67I | Micrococcus sp. MS67 | CCNGG | 2 | | | MspA1I | Moraxella sp. A1 | CMGCKG | 3 | | | MspB4I | Moraxella sp. B4 | GGYRCC | 1 | AccB1I, BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, PfaAI | | MspCI | Micrococcus sp. | CTTAAG | 1 | | | MspR9I | Micrococcus sp. R9 | CCNGG | 2 | | | MspSWI | Moraxella sp. SW | ATTTAAAT | 4 | | | MspV281I | Myxosarcinia sp. V/281 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I, BsiHKAI,  Bsm6I, HgiAI,  HpyF46II, | | MspYI | Microcystis sp. J2 | YACGTR | 3 | | | MssI | Methylobacterium sp. Dd 5-732 | GTTTAAAC | 4 | PmeI | | MstI | Microcoleus sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, NsbI, PamI, Pun14627I | | MstII | Microcoleus sp. | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | | MthZI | Methanobacterium thermoformicicum Z-245 | CTAG | 1 | | | MunI | Mycoplasma sp. | CAATTG | 1 | | | MvaI | Micrococcus varians RFL19 | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, Bst2UI, SslI, TaqXI, ZanI | | Mva1269I | Micrococcus varians RFL1269 | GAATGC | 7 | Asp26HI, Asp40HI, Asp50HI, BscCI, BsmI, Mva1269I, PctI | | MvnI | Methanococcus vannielii | CGCG | 2 | AccII, Bsh1236I, BstFNI, BtkI, Csp68KVI, FalII, FauBII, ThaI | | MvrI | Micrococcus varians | CGATCG | 4 | Afa22MI, BspCI, EagBI, ErhB9I, Ple19I, PvuI, RshI, XorII | | MxaI | Myxococcus xanthus F18E | GAGCTC | 3 | | | NaeI | Nocardia aerocolonigenes | GCCGGC | 3 | | | NarI | Nocardia argentinensis | GGCGCC | 2 | | | NblI | Nocardia blackwellii | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, MvrI, Ple19I, Psu161I, RshI, XorII | | NciI | Neisseria cinerea | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, EcoHI, HgiS22I, Mgl14481I | | NcoI | Nocardia corallina | CCATGG | 1 | | | NcrI | Nocardia carnea C-212 | AGATCT | 1 | | | NcuI | Neisseria cuniculi | GAAGA | 9 | | | NdaI | Nocardia dassonvillei | GGCGCC | 2 | | | NdeI | Neisseria denitrificans | CATATG | 2 | | | NdeII | Neisseria denitrificans | GATC | 1 | Bce243I, Bsp105I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, Sth368I | | NgoAIII | Neisseria gonorrhoeae FA1090 | CCGCGG | 4 | | | NgoAIV | Neisseria gonorrhoeae FA1090 | GCCGGC | 1 | | | NgoMIV | Neisseria gonorrhoeae MS11 | GCCGGC | 1 | | | NgoPII | Neisseria gonorrhoeae P9-2 | GGCC | 2 | | | NgoPIII | Neisseria gonorrhoeae P9-2 | CCGCGG | 4 | | | NheI | Neisseria mucosa heidelbergensis | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, LlaG2I, PstNHI | | NlaII | Neisseria lactamica | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | | NlaIII | Neisseria lactamica | CATG | 4 | | | NlaIV | Neisseria lactamica | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, PspN4I | | Nli3877I | Nostoc linckia | CYCGRG | 5 | Ama87I, AvaI, BcoI, BsiHKCI, Eco27kI, Eco88I, NspSAI, OfoI | | NmeCI | Neisseria meningitidis C114 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | | NmeRI | Neisseria meningitidis | CAGCTG | 3 | | | NmuCI | Neisseria mucosa C9-2 | GTSAC | 1 | | | NopI | Nocardia opaca | GTCGAC | 1 | | | NotI | Nocardia otitidis-caviarum | GCGGCCGC | 2 | | | NphI | Neisseria pharyngis C245 | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, RalF40I, Sau3AI | | NruI | Nocardia rubra | TCGCGA | 3 | | | NsbI | Neisseria subflava Va-1 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, PamI, Pun14627I | | NsiI | Neisseria sicca | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | | NsiCI | Neisseria sicca C351 | GATATC | 3 | | | NspI | Nostoc sp. C | RCATGY | 5 | | | NspII | Nostoc sp. C | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, MhlI, NspII, SduI | | NspIII | Nostoc sp. C | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, Eco88I, OfoI, PunAI | | NspIV | Nostoc sp. C | GGNCC | 1 | AvcI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | | NspV | Nostoc sp. C | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, PlaII, SspRFI | | Nsp7121I | Nostoc sp. 7121 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | | Nsp29132II | Nostoc sp. | GGATCC | 1 | AliI, ApaCI, BamHI, Bce751I, Nsp29132II, Pfl8I, SolI, Uba4009I | | NspBII | Nostoc sp. | CMGCKG | 3 | | | NspHI | Nostoc sp. | RCATGY | 5 | | | NspLKI | Nocardia sp. LK | GGCC | 2 | | | NspMACI | Nostoc sp. | AGATCT | 1 | | | NspSAI | Nostoc sp. SA | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | | NspSAII | Nostoc sp. SA | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BseT10I, BstPI, Eco91I, NspSAII, PspEI | | NspSAIV | Nostoc sp. SA | GGATCC | 1 | AliI, BamHI, Bsp98I, Bsp4009I, NspSAIV, Pfl8I, SolI, Uba4009I | | NunII | Nocardia uniformis | GGCGCC | 2 | |","Markdown" "Bioengineering","telatin/seqfu2","re/scrape.py",".py","4210","146","#!/usr/bin/env python3 """""" Extract enzyme table from wikipedia page. Input: a text file with the list of Enzyme tables URLs Internal use only / Dev """""" #Note: requires lxml import pandas as pd from bs4 import BeautifulSoup from urllib.request import urlopen import re import os, sys def siteString(site): # site: 5' GAATTC 3' CTTAAG # cutsite: 5' ---G AATTC--- 3' 3' ---CTTAA G--- 5' if not isinstance(site, str): return """" # Extract the string from ""5'"" to ""3'"" regex = ""5'(.*?)3'"" # Find the cutsite cutsite = re.search(regex, site).group(1) # Strip leadingnad trailing whitespaces if re.search(""\d"", cutsite): print(f""Warning: {cutsite} site contains a number"", file=sys.stderr) return """" return cutsite.strip() def cutPosition(string): #5' ---AT CGAT--- 3' regex = ""5' [-]+(.+) (.+)[-]+ 3'"" # Capture the two groups match = re.search(regex, string) if match: return len(match.group(1))#, match.group(2) else: return -1 def getTable(url, class_attributes=None, columnName=""Enzyme""): if class_attributes is None: class_attributes = [] # Get the page from url if url.lower().startswith(""http""): page = BeautifulSoup(urlopen(url), ""html.parser"") #nosec - was checked above else: raise ValueError(""url must start with http"") # Select tables containing all attributes in the list class_attributes tables = page.find_all(""table"", class_=class_attributes) # Select the table from tables having columnName as column name tables = [table for table in tables if columnName in table.find_all(""tr"")[0].text] # Return the table return tables def htmlTableToDataFrame(table): # Create a dataframe from the table df = pd.read_html(str(table))[0] # First row is the header df.columns = df.iloc[0] # Drop the first row df = df.drop(df.index[0]) # First column is the enzyme name (index) df.index = df.iloc[:,0] # Drop the first column df = df.drop(df.columns[0], axis=1) return df def urlToDf(url): tables = getTable(url, [""sortable""], ""Enzyme"") dfs = [] for table in tables: df = htmlTableToDataFrame(table) # From the first column strip the pattern ""\[.*\]"" df.index = df.index.str.replace(""\[.*\]"", """") # Columns to remove colToRemove = [""PDB code""] # Check if colToRemove are in the dataframe for col in colToRemove: if col in df.columns: df = df.drop(col, axis=1) # Replace column ""Recognition sequence"" with siteString() df[""Recognition sequence""] = df[""Recognition sequence""].apply(siteString) # Remove rows where ""Recognition sequence"" is empty df = df[df[""Recognition sequence""] != """"] # Replace ""Cut"" with cutPosition() df[""Cut""] = df[""Cut""].apply(cutPosition) # Drop rows where ""Cut"" is -1 df = df[df[""Cut""] != -1] dfs.append(df) df = pd.concat(dfs) return df if __name__ == ""__main__"": inputfile = sys.argv[-1] if not os.path.exists(inputfile): print(""ERROR: file not found: "", inputfile) sys.exit(1) # Load list of urls from file with open(inputfile, ""r"") as f: urls = f.readlines() dataframes = [] for url in urls: if not url.lower().startswith(""http""): continue basename = os.path.basename(url) # Strip after ""#"" if ""#"" in basename: basename = basename.split(""#"")[0] if "":_"" in basename: basename = basename.split("":_"")[1] try: df = urlToDf(url) print(basename, df.shape, file=sys.stderr) # Replace nan values with empty string df = df.fillna("""") df.to_markdown(basename + "".md"") dataframes.append(df) except Exception as e: print(e) if len(dataframes) > 0: df = pd.concat(dataframes) print(df.shape) df.to_markdown(""enzyme_table.md"") df.to_csv(""enzyme_table.csv"") ","Python" "Bioengineering","telatin/seqfu2","src/build.md",".md","1800","71","# Initial build script ```bash #!/bin/bash set -exuo pipefail OLDWD=$PWD PLATFORM="""" if [[ $(uname) == 'Darwin' ]]; then PLATFORM=""_mac"" fi DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" nim --version >/dev/null 2>&1 || { echo ""nim compiler not found.""; exit 1; } RELEASE="""" if [ ""${NIM_RELEASE+x}"" ]; then RELEASE="" -d:release ""; fi nim c --hints:off -w:on --opt:speed $RELEASE -p:$DIR/lib -o:$DIR/../bin/seqfu${PLATFORM} $DIR/sfu.nim \ || { echo ""Compilation failed.""; exit 1; } for UTIL in src/fu*.nim; do NAME=$(basename ${UTIL%.nim} | sed 's/_/-/g') THREADS="""" if [[ $(grep thread ""$UTIL"") ]]; then THREADS="" --threads:on "" fi nim c $THREADS --hints:off -w:on --opt:speed $RELEASE -p:$DIR/lib -o:$DIR/../bin/${NAME}${PLATFORM} $UTIL \ || { echo ""Util ${NAME} compilation failed.""; exit 2; } done if [ -e ""$DIR/../test/mini.sh"" ]; then bash $DIR/../test/mini.sh else echo ""Minimal test suite not found at: $DIR/../test/mini.sh"" exit 1; fi VERSION=$(grep return $DIR/seqfu_utils.nim | grep -o \\d\[^\""\]\\+ | head -n 1) sed -i ""s/version\s\+=\s\+\"".\+\""/version = \""$VERSION\""/"" $DIR/../seqfu.nimble || true perl -e ' $VERSION=shift(@ARGV); $BIN=shift(@ARGV); $SPLASH=`$BIN --help 2>&1`; $TEMPLATE=shift(@ARGV); print STDERR ""bin:$BIN;version:$VERSION\n""; open(I, ""<"", $TEMPLATE); while () { while ( $_=~/\{\{ (\w+) \}\}/g ) { $repl=${$1}; $match=$1; $_=~s/\{\{\s*$match\s*\}\}/$repl/g; } print; } print ""## Some functions\n""; for my $function (""head"", ""interleave"", ""deinterleave"", ""derep"", ""stats"", ""count"") { print ""\n### :closed_book: seqfu $function\n\n""; print ""```\n""; print `$BIN $function --help`; print ""```\n"" } ' ""$VERSION"" ""$DIR/../bin/seqfu${PLATFORM}"" ""$DIR/README.raw"" > $DIR/../README.md ```","Markdown" "Bioengineering","telatin/seqfu2","src/countseqs.sh",".sh","697","36","#!/bin/bash CAT=""cat"" # Check if the first parameter was passed if [ -z ""$1"" ]; then echo ""Usage: countseqs.sh "" exit 1 fi # Check if the file exists if [ ! -f ""$1"" ]; then echo ""File $1 does not exist"" exit 1 fi # Check if the filename ends with .gz if [[ ""$1"" == *.gz ]]; then #GZIPPED=1 GUNZIP_PIPE=""gzip -d "" else #GZIPPED=0 GUNZIP_PIPE=""$CAT"" fi # Get the first character of the file FIRST_CHAR=$($CAT ""$1"" | $GUNZIP_PIPE | head -c 1) if [[ ""$FIRST_CHAR"" == "">"" ]]; then COUNT=$($CAT ""$1"" | $GUNZIP_PIPE | grep -c ""^>"") elif [[ ""$FIRST_CHAR"" == ""@"" ]]; then COUNT=$($CAT ""$1"" | $GUNZIP_PIPE | wc -l) COUNT=$((COUNT / 4)) fi echo $COUNT ","Shell" "Bioengineering","telatin/seqfu2","src/doc/bench.md",".md","236","5","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | |:---|---:|---:|---:|---:| | `perl uniq.pl ./input/*.fa*` | 935.7 ± 38.4 | 886.1 | 1027.9 | 8.39 ± 0.36 | | `derep_Darwin ./input/*.fa*` | 111.5 ± 1.6 | 108.9 | 115.1 | 1.00 | ","Markdown" "Bioengineering","telatin/seqfu2","src/doc/single_file.md",".md","415","6","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | |:---|---:|---:|---:|---:| | `vsearch --derep_fulllength ./input/filt.fa.gz --output /tmp/vsearch.fa` | 179.1 ± 9.6 | 170.1 | 198.0 | 1.06 ± 0.10 | | `./bin/derep_Darwin ./input/filt.fa.gz > /tmp/derep.fa` | 169.2 ± 13.1 | 150.0 | 211.8 | 1.00 | | `perl ./test/uniq.pl ./input/filt.fa.gz > /tmp/uniq.fa ` | 956.9 ± 64.5 | 866.4 | 1063.1 | 5.65 ± 0.58 | ","Markdown" "Bioengineering","telatin/seqfu2","src/doc/build-seqfu.sh",".sh","110","7","#!/bin/bash mkdir -p ""${PREFIX}""/bin chmod +x ./bin/* mv ./bin/* ""${PREFIX}""/bin/ mv seqfu ""${PREFIX}""/bin/ ","Shell" "Bioengineering","telatin/seqfu2","test/test-rotate.sh",".sh","974","29","#!/bin/bash ROTATE=$(""$BINDIR""/seqfu rotate -i 14 ""$FILES""/homopolymer.fa| grep -v '^>') FORROT=$(""$BINDIR""/seqfu rotate -m AAAAAAAAAAC ""$FILES""/homopolymer.fa| grep -v '^>') REVROT=$(""$BINDIR""/seqfu rotate -r -m GTTTTTTT ""$FILES""/homopolymer.fa| grep -v '^>') if [[ $ROTATE = ""AAAAAAAAAACTGCTACTAACACGTACTACTG"" ]]; then echo -e ""$OK: sequence rotated"" PASS=$((PASS+1)) else echo -e ""$FAIL: rotated seq $ROTATE should start with polyA"" ERRORS=$((ERRORS+1)) fi if [[ $FORROT = ""AAAAAAAAAACTGCTACTAACACGTACTACTG"" ]]; then echo -e ""$OK: sequence rotated with pattern"" PASS=$((PASS+1)) else echo -e ""$FAIL: rotated seq $ROTATE (pattern) should start with polyA"" ERRORS=$((ERRORS+1)) fi if [[ $REVROT = ""GTTTTTTTTTTCAGTAGTACGTGTTAGTAGCA"" ]]; then echo -e ""$OK: sequence rotated with reverse pattern"" PASS=$((PASS+1)) else echo -e ""$FAIL: rotated seq $ROTATE (reverse pattern) should start with GTTT."" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-tab.sh",".sh","3794","111","#!/bin/bash export SEQFU_QUIET=1 SE=$(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fastq | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | ""$BINDIR""/seqfu cnt | cut -f 2) if [[ $SE == ""5"" ]]; then echo -e ""$OK: FASTQ sequence tabulated / detabulated"" PASS=$((PASS+1)) else echo -e ""$FAIL: FASTQ sequence tabulated / detabulated 5 expected, got $SE"" ERRORS=$((ERRORS+1)) fi FA=$(""$BINDIR""/seqfu tabulate ""$FILES""/numbers.fa | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | ""$BINDIR""/seqfu cnt | cut -f 2) if [[ $FA == ""1000"" ]]; then echo -e ""$OK: FASTA sequence tabulated / detabulated"" PASS=$((PASS+1)) else echo -e ""$FAIL: FASTA sequence tabulated / detabulated 1000 expected, got $FA"" ERRORS=$((ERRORS+1)) fi ILVCOUNT=$(""$BINDIR""/seqfu tabulate ""$FILES""/interleaved.fq.gz -i | wc -l | grep -o '[[:digit:]]\+') if [[ $ILVCOUNT == ""7"" ]]; then echo -e ""$OK: FQ interleaved sequence tabulated / detabulated"" PASS=$((PASS+1)) else echo -e ""$FAIL: FQ interleaved sequence tabulated / detabulated 7 PAIRS (lines) expected, got $ILVCOUNT"" ERRORS=$((ERRORS+1)) fi ILV=$(""$BINDIR""/seqfu tabulate ""$FILES""/interleaved.fq.gz -i | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | ""$BINDIR""/seqfu cnt | cut -f 2) if [[ $ILV == ""14"" ]]; then echo -e ""$OK: FQ interleaved sequence tabulated / detabulated"" PASS=$((PASS+1)) else echo -e ""$FAIL: FQ interleaved sequence tabulated / detabulated 14 expected, got $ILV"" ERRORS=$((ERRORS+1)) fi ## FASTQ SE SE_LINES=$(getnumber $(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fastq | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | wc -l)) if [[ $SE_LINES == ""20"" ]]; then echo -e ""$OK: FASTQ output format: line count $SE_LINES"" PASS=$((PASS+1)) else echo -e ""$FAIL: FASTQ output format: line count 20 expected, got $SE_LINES"" ERRORS=$((ERRORS+1)) fi ## FASTQ PE SE_LINES=$(getnumber $(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fastq | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | wc -l)) if [[ $SE_LINES == ""20"" ]]; then echo -e ""$OK: FASTQ output format: line count $SE_LINES"" PASS=$((PASS+1)) else echo -e ""$FAIL: FASTQ output format: line count 20 expected, got $SE_LINES"" ERRORS=$((ERRORS+1)) fi ## FASTA SE FA_LINES=$(getnumber ""$(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fasta | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | wc -l)"") if [[ $FA_LINES == ""8"" ]]; then echo -e ""$OK: FASTA output format: $FA_LINES"" PASS=$((PASS+1)) else echo -e ""$FAIL: FASTA output format: 8 expected, got $FA_LINES"" ERRORS=$((ERRORS+1)) fi ## Pair end? TEMPORARY_DIR=$(mktemp -d) ""$BINDIR""/seqfu tabulate -i ""$FILES""/interleaved.fq.gz > ""$TEMPORARY_DIR""/interleaved.tabcheck EXP=8 GOT=$(getnumber ""$(""$BINDIR""/fu-tabcheck ""$TEMPORARY_DIR""/interleaved.tabcheck | cut -f 3)"") if [[ $GOT == ""$EXP"" ]]; then echo -e ""$OK: Tabulated file has $EXP columns: $GOT"" PASS=$((PASS+1)) else echo -e ""$FAIL: Tabulated file has not $EXP columns: $GOT"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu tabulate -d ""$TEMPORARY_DIR""/interleaved.tabcheck| ""$BINDIR""/seqfu deinterleave -o ""$TEMPORARY_DIR""/dei - EXP=7 GOT=$(getnumber ""$(""$BINDIR""/seqfu cnt -u ""$TEMPORARY_DIR""/dei_R1.fq | cut -f 2)"") if [[ $GOT == ""$EXP"" ]]; then echo -e ""$OK: Deinterleaved detabulated has $EXP R1 reads: $GOT"" PASS=$((PASS+1)) else echo -e ""$FAIL: Deinterleaved detabulated has not $EXP R1 reads: $GOT"" ERRORS=$((ERRORS+1)) fi GOT=$(getnumber ""$(""$BINDIR""/seqfu cnt -u ""$TEMPORARY_DIR""/dei_R2.fq | cut -f 2)"") if [[ $GOT == ""$EXP"" ]]; then echo -e ""$OK: Deinterleaved detabulated has $EXP R2 reads: $GOT"" PASS=$((PASS+1)) else echo -e ""$FAIL: Deinterleaved detabulated has not $EXP R2 reads: $GOT"" ERRORS=$((ERRORS+1)) fi rm -rf ""$TEMPORARY_DIR"" ","Shell" "Bioengineering","telatin/seqfu2","test/interleave.md",".md","3856","115","# Reference interleave.sh script ```bash #!/bin/bash DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" PLATFORM="""" if [[ $(uname) == ""Darwin"" ]]; then PLATFORM="""" fi BIN=$DIR/../bin/seqfu${PLATFORM} FILES=$DIR/../data/ # iPair1=$FILES/illumina_1.fq.gz iPair2=$FILES/illumina_2.fq.gz iPair1a=$FILES/tests/sample1_R1.fq iPair1b=$FILES/tests/sample1_R2.fq iPair1b=$FILES/tests/sample1_forward.fq iPair2b=$FILES/tests/sample1_reverse.fq iR1LONG1=$FILES/tests/longerone_R1.fq iR2LONG1=$FILES/tests/longerone_R2.fq iR1LONG2=$FILES/tests/longertwo_R1.fq iR2LONG2=$FILES/tests/longertwo_R2.fq iR1EMPTY=$FILES/tests/empty_R1.fq iR2EMPTY=$FILES/tests/empty_R2.fq iAllMISS=$FILES/tests/nonexistent.fq ERRORS=0 echo ""# Testing -interleave- function"" # Binary works $BIN > /dev/null|| { echo ""Binary not working""; exit 1; } echo ""OK: Running"" # Interleave normal R1 and R2 fastq echo """" echo ""1. TEST - interleave R1 and R2 fastq"" echo ""COMMAND: $BIN ilv -v -o testtmpSample1.fq -1 $iPair1a -2 $iPair2a"" $BIN ilv -v -o testtmpSample1.fq -1 $iPair1a -2 $iPair2a if [[ $(cat testtmpSample1.fq | wc -l) == $(cat $iPair1a $iPair1a | wc -l ) ]]; then echo ""OK: Interleave fastq _R1 and _R2"" else echo ""ERR: Interleave fastq _R1 and _R2"" ERRORS=$((ERRORS+1)) fi # Interleave normal gzipped - find _2 by only giving _1 echo """" echo ""2. TEST - interleave gesipped fastq - _1 and let _2 automatically find"" echo ""COMMAND: BIN ilv -v -o testtmpS1.fq -1 $iPair1"" $BIN ilv -v -o testtmpS1.fq -1 $iPair1 if [[ $(cat testtmpS1.fq | wc -l) == $(cat $iPair1 $iPair2 | gunzip | wc -l ) ]]; then echo ""OK: Interleave fastq _1 and _2"" else echo ""ERR: Interleave fastq _1 and _2"" ERRORS=$((ERRORS+1)) fi # Interleave normal custom extension echo """" echo ""3. TEST - interleave _forward and let _reverse automatically find by specifying -f and -r "" echo ""COMMAND: $BIN ilv -v -o testtmpS2.fq -1 $iPair1b -f forward -r reverse"" $BIN ilv -v -o testtmpS2.fq -1 $iPair1b -f forward -r reverse if [[ $(cat testtmpS2.fq | wc -l) == $(cat $iPair1b $iPair2b | wc -l ) ]]; then echo ""OK: Interleave fastq _forward and _reverse"" else echo ""ERR: Interleave fastq _forward and _reverse"" ERRORS=$((ERRORS+1)) fi # Interleave unbalanced reads echo """" echo ""4. TEST - interleave R1 (more reads) and R2 (fewer reads) of fastq"" echo ""COMMAND: $BIN ilv -v -o testtmpLong1.fq -1 $iR1LONG1 -2 $iR2LONG1 2> testtmpnope"" $BIN ilv -v -o testtmpLong1.fq -1 $iR1LONG1 -2 $iR2LONG1 # Interleave unbalanced reads echo """" echo ""5. TEST - interleave R1 (fewer reads) and R2 (more reads) of fastq"" echo ""COMMAND: $BIN ilv -v -o testtmpLong2.fq -1 $iR1LONG2 -2 $iR2LONG2 2> testtmpnope2"" $BIN ilv -v -o testtmpLong2.fq -1 $iR1LONG2 -2 $iR2LONG2 # Interleave two same fastq # FATAL ERROR: First file and second file are equal. echo """" echo ""6. TEST - interleave two same fastq files"" echo ""COMMAND: $BIN ilv -v -1 $iPair1a -2 $iPair1a"" $BIN ilv -v -1 $iPair1a -2 $iPair1a # Interleave two empty fastq # needed: warning if input files are empty ""no sequenes in file X""; at the moment: produces empty output but no warning echo """" echo ""7. TEST - interleave two empty fastq files"" echo ""COMMAND: $BIN ilv -v -o testtmpintempty.fq -1 $iR1EMPTY -2 $iR2EMPTY"" $BIN ilv -v -o testtmpintempty.fq -1 $iR1EMPTY -2 $iR2EMPTY if [[ $(cat testtmpintempty.fq | wc -l ) == "" 0"" ]]; then echo ""OK: Two empty input files resulted in one empty output file"" else echo ""ERR: interleave two empty fastq files"" ERRORS=$((ERRORS+1)) fi # Interleave nonexistent R2 # needed: warning if input R2 file is nonexistent; at the moment: error #echo """" #echo ""8. TEST - interleave one existent R1 fastq file with one non-existent file"" #echo ""COMMAND: $BIN ilv -v -o testtmpmiss -1 $iPair1a -2 $iAllMISS"" #$BIN ilv -v -o testtmpmiss -1 $iPair1a -2 $iAllMISS rm testtmp* ``` ","Markdown" "Bioengineering","telatin/seqfu2","test/build.bash",".bash","63","3","nim c speed/imported.nim nim c -p:../src/lib speed/native.nim ","Bash" "Bioengineering","telatin/seqfu2","test/bin.sh",".sh","845","36","#!/bin/bash SCRIPT_DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" && pwd )"" echo ""Building fresh binary"" echo ""============================="" VER=$(curl -s https://api.github.com/repos/telatin/seqfu2/releases/latest | perl -nE ' my ($tag, $val) = split /:/, $_; if ($tag=~/tag_name/) { my @tag = split /""/, $val; for my $i (@tag) { $i =~s/[^0-9.]//g; say $i if (length($i) > 2); } }') if [[ $(uname) == ""Darwin"" ]]; then PLAT='Darwin'; else PLAT='Linux-x86_64' fi DEST=""$SCRIPT_DIR/../releases/zips/""; mkdir -p ""$DEST"" echo ""Last version online: $VER"" echo ""Local version: $LOCALVER"" nimble build LOCAL_RELEASE=$(./bin/seqfu version) zip -r ""$DEST""/SeqFu-v""${LOCAL_RELEASE}""-""${PLAT}"".zip bin/* echo ""Last version online: $VER"" echo ""Local version: $LOCAL_RELEASE"" echo ""$DEST/SeqFu-v${LOCAL_RELEASE}-${PLAT}.zip""","Shell" "Bioengineering","telatin/seqfu2","test/test-bases.sh",".sh","3604","141"," #!/bin/bash export SEQFU_QUIET=1 TEMPFILENAME=$(mktemp) ### SINGLE END ""$BINDIR""/seqfu bases ""$FILES""/{base,base_extra,bases_lower}.fa > ""$TEMPFILENAME"" ""$BINDIR""/seqfu bases -c ""$FILES""/{base,base_extra,bases_lower}.fa > ""$TEMPFILENAME.raw"" ""$BINDIR""/seqfu bases ""$FILES""/upper-{lower,none,only}.fa > ""$TEMPFILENAME.upper"" WC=$(getnumber $(cat ""$TEMPFILENAME"" | wc -l)) MSG=""Counted files"" EXP=3 if [[ $EXP == $WC ]]; then echo -e ""$OK: $MSG (expected $EXP, got $WC)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $WC)"" ERRORS=$((ERRORS+1)) fi # Check table ""$BINDIR""/fu-tabcheck ""$TEMPFILENAME"" > ""$TEMPFILENAME.check"" IS_TABLE=$(cat ""$TEMPFILENAME.check"" | cut -f 2) NUM_COLS=$(getnumber $(cat ""$TEMPFILENAME.check"" | cut -f 3)) MSG=""Output is a table"" EXP=""Pass"" if [[ $EXP == $IS_TABLE ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_TABLE)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_TABLE)"" ERRORS=$((ERRORS+1)) fi MSG=""Output is a table with 9 columns"" EXP=10 if [[ $EXP == $NUM_COLS ]]; then echo -e ""$OK: $MSG (expected $EXP, got $NUM_COLS)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $NUM_COLS)"" ERRORS=$((ERRORS+1)) fi ### RAw checks MSG=""Raw counts of extra bases"" EXP=10 GOT=$(getnumber $(cat ""$TEMPFILENAME.raw"" | grep extra | cut -f 8 )) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi MSG=""Raw counts of lowercase bases"" EXP=15 GOT=$(getnumber $(cat ""$TEMPFILENAME.raw"" | grep lower | cut -f 2 )) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi #/// MSG=""Count ratio of As in bases_lower"" EXP=""33.33"" GOT=$(cat ""$TEMPFILENAME"" | grep lower | cut -f 3 ) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi MSG=""Count ratio of As in base.fa"" EXP=""50.00"" GOT=$(cat ""$TEMPFILENAME"" | grep base.fa | cut -f 3 ) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi MSG=""Count ratio of Gs in base.fa"" EXP=""0.00"" GOT=$(cat ""$TEMPFILENAME"" | grep base.fa | cut -f 5 ) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi MSG=""Uppercase ratio: none"" EXP=""0.00"" GOT=$(cat ""$TEMPFILENAME.upper"" | grep none | cut -f 10 ) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi MSG=""Uppercase ratio: all"" EXP=""100.00"" GOT=$(cat ""$TEMPFILENAME.upper"" | grep only | cut -f 10 ) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi MSG=""Uppercase ratio: mixed"" EXP=""50.00"" GOT=$(cat ""$TEMPFILENAME.upper"" | grep lower | cut -f 10 ) if [[ $EXP == $GOT ]]; then echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" ERRORS=$((ERRORS+1)) fi rm ""$TEMPFILENAME""*","Shell" "Bioengineering","telatin/seqfu2","test/compare-grep.sh",".sh","311","15","#!/bin/bash for FILE in data/numbers.fa data/filt.fa.gz; do for PATTERN in 12$ filt.598..; do for SWITCH in ""-w"" ""-f""; do echo ""=== $PATTERN $SWITCH"" hyperfine ""bin/seqfu grep $SWITCH -r $PATTERN $FILE"" \ ""bin/seqfu grep2 $SWITCH -r $PATTERN $FILE"" done done done ","Shell" "Bioengineering","telatin/seqfu2","test/test-index.sh",".sh","2975","131","#!/bin/bash # Single file TMP=$(mktemp) echo "" Temp file: $TMP"" ""$BINDIR""/fu-index ""$iPair1"" ""$iPair2"" > ""$TMP"" MSG=""Checking output expecting 2 lines:"" EXP=2 OBS=$(cat ""$TMP"" | wc -l | grep -o ""[[:digit:]]\+"" | head -n 1) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" cat ""$TMP"" echo --- #cat ""$TMP"" | wc -l | '[[:digit:]]\+' ERRORS=$((ERRORS+1)) fi MSG=""Got expected index:"" EXP=""TACGCTGC+CTATTAAG"" OBS=$(cat ""$TMP"" | cut -f 2 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: $EXP / $OBS"" ERRORS=$((ERRORS+1)) fi MSG=""Got expected index ratio:"" EXP=""1.00"" OBS=$(cat ""$TMP"" | cut -f 3 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" ERRORS=$((ERRORS+1)) fi MSG=""Got expected pass:"" EXP=""PASS"" OBS=$(cat ""$TMP"" | cut -f 4 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" ERRORS=$((ERRORS+1)) fi MSG=""Got expected instrument:"" EXP=""A00709"" OBS=$(cat ""$TMP"" | cut -f 5 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" ERRORS=$((ERRORS+1)) fi MSG=""Got expected flowcell:"" EXP=""HYG25DSXX"" OBS=$(cat ""$TMP"" | cut -f 7 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" ERRORS=$((ERRORS+1)) fi # --- ""$BINDIR""/fu-index ""$iAmpli"" > ""$TMP"" MSG=""Checking output expecting 1 line:"" EXP=1 OBS=$(wc -l ""$TMP"" | grep -o '[[:digit:]]\+' | head -n 1) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP / got=$OBS"" ERRORS=$((ERRORS+1)) fi MSG=""Checking failed sample (no index):"" EXP="""" OBS=$(cat ""$TMP"" | cut -f 2 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e """"$FAIL: $MSG: $EXP / $OBS: $(cat $TMP)"""" ERRORS=$((ERRORS+1)) fi MSG=""Checking failed sample (status):"" EXP=""--"" OBS=$(cat ""$TMP"" | cut -f 4 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e """"$FAIL: $MSG: $EXP / $OBS: $(cat $TMP)"""" ERRORS=$((ERRORS+1)) fi # --- ""$BINDIR""/fu-index ""$FILES""/mixed_index.fq.gz > ""$TMP"" MSG=""Checking failed sample (ratio):"" EXP=""0.50"" OBS=$(cat ""$TMP"" | cut -f 3 | sort | uniq) if [[ ""$OBS"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG: $EXP / $OBS"" PASS=$((PASS+1)) else echo -e """"$FAIL: $MSG: $EXP / $OBS: $(cat $TMP)"""" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-orflegacy.sh",".sh","1388","45","#!/bin/bash ORFFOR=$(""$BINDIR""/fu-orf ""$FILES""/orf.fa.gz --min-size 500 | grep "">"" | wc -l) ORFREV=$(""$BINDIR""/fu-orf ""$FILES""/orf.fa.gz --min-size 500 --scan-reverse | grep "">"" | wc -l) if [[ $ORFFOR -eq 1 ]]; then echo -e ""$OK: ONE large ORF found in forward mode"" PASS=$((PASS+1)) else echo -e ""$FAIL: Expected ONE large ORF found in forward mode [found: $ORFFOR]"" ERRORS=$((ERRORS+1)) fi if [[ $ORFREV -eq 2 ]]; then echo -e ""$OK: Two large ORFs found in for/rev mode"" PASS=$((PASS+1)) else echo -e ""$FAIL: Expected Two large ORFs found in forward/reverse mode [found: $ORFREV]"" ERRORS=$((ERRORS+1)) fi CODE1=$(""$BINDIR""/fu-orf ""$FILES""/codons.fa --min-size 3 --min-read-len 6 -c 1 | grep -v "">"") CODE5=$(""$BINDIR""/fu-orf ""$FILES""/codons.fa --min-size 3 --min-read-len 6 -c 5 | grep -v "">"") if [[ $CODE1 != $CODE5 ]]; then PASS=$((PASS+1)) echo -e ""$OK: Genetic code implemented"" else echo -e ""$FAIL: Genetic code match $CODE1 $CODE5"" ERRORS=$((ERRORS+1)) fi if [[ $CODE1 =~ ""RRI"" ]]; then echo -e ""$OK: Standard genetic code [1]"" PASS=$((PASS+1)) else echo -e ""$FAIL: Standard genetic code error $CODE1 != RRI"" ERRORS=$((ERRORS+1)) fi if [[ $CODE5 =~ ""SSM"" ]]; then echo -e ""$OK: Genetic code #5"" PASS=$((PASS+1)) else echo -e ""$FAIL: Genetic code 5 error $CODE5 != SSM"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/merge.md",".md","234","5","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | |:---|---:|---:|---:|---:| | `seqfu merge -o /tmp/ data/lane` | 2.6 ± 0.9 | 1.6 | 10.4 | 1.00 | | `bash /tmp/merge.sh data/lane/` | 31.8 ± 4.0 | 25.4 | 49.5 | 12.42 ± 4.46 | ","Markdown" "Bioengineering","telatin/seqfu2","test/test-cat.sh",".sh","1816","78","#!/bin/bash # Single file TMP=$(mktemp) ""$BINDIR""/seqfu stats --basename ""$iAmpli"" > ""$TMP"" MSG=""Precheck input file has 1000 sequences"" if [[ $(count ""$FILES""/numbers.fa) == 1000 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu cat --skip 2 ""$FILES""/numbers.fa > ""$TMP"" OBS=$(count ""$TMP"") EXP=500 MSG=""Checking cat --skip 2, expecting 500 sequences, got $OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu cat --skip-first 500 --skip 2 ""$FILES""/numbers.fa > ""$TMP"" OBS=$(count ""$TMP"") EXP=250 MSG=""Checking cat --skip 2 and --skip-first 500, expecting $EXP sequences, got $OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu cat --skip-first 500 --skip 2 ""$FILES""/numbers.fa > ""$TMP"" OBS=$(count ""$TMP"") EXP=250 MSG=""Checking cat --skip 2 and --skip-first 500, expecting $EXP sequences, got $OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu cat --skip-first 500 --max-bp 200 --skip 2 ""$FILES""/numbers.fa > ""$TMP"" OBS=$(bp ""$TMP"") EXP=200 MSG=""Checking --max-bp 200, got $OBS <= $EXP"" if [[ ! $OBS -gt $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu cat --jump-to 500 ""$FILES""/numbers.fa > ""$TMP"" OBS=$(count ""$TMP"") EXP=500 MSG=""Checking --jump-to NAME (exclusive), got $OBS expecting $EXP"" if [[ ! $OBS -gt $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/minimal-markdown-linter.py",".py","3485","118","#!/usr/bin/env python """""" Read a Markdown file and save it back out, but with some minimal changes to make it pass the Markdown linter. """""" import sys import os def eprint(*args, **kwargs): print(*args, file=sys.stderr, **kwargs) def remove_trailing_whitespace(lines): """""" Remove trailing space from a line. """""" lines = [line.rstrip() for line in lines] return lines def fenced_code_blocks(lines): """""" Fenced code blocks should be surrounded by blank lines """""" opened = False for i in range(len(lines)): if lines[i].startswith('```'): if i == 0 or lines[i-1] != '': if not opened: lines.insert(i, '') opened = True continue elif i == len(lines)-1 or lines[i+1] != '': if opened: lines.insert(i+1, '') opened = False continue return lines def headerlines_withspace(lines): """""" Markdown headers have a variable number of '#' and after a space must be present """""" for index in range(len(lines)): line = lines[index] if line.startswith('#'): for pos, char in enumerate(line): if char != '#' and line[pos+1] != ' ': lines[index] = line[:pos] + ' ' + line[pos:] break return lines def headerlines_surrounded(lines): """""" Headers should be surrounded by blank lines """""" for i in range(len(lines)): if lines[i].startswith('##'): if i == 0 or lines[i-1] != '': lines.insert(i, '') if i == len(lines)-1 or lines[i+1] != '': lines.insert(i+1, '') return lines def long_lines(lines): """""" Split long lines to be no longer than 60 characters """""" for L in range(len(lines)): if len(lines[L]) > 60: for i, char in enumerate(lines[L]): if char == ' ' or char == '\t': lastwhite = i if i > 60: # replace character lastwhite with a newline lines[L] = lines[L][:lastwhite] lines.insert(L+1, lines[L][lastwhite+1:]) break return lines if __name__ == '__main__': import argparse parser = argparse.ArgumentParser(description=__doc__) parser.add_argument('infile', nargs='+', type=argparse.FileType('r')) parser.add_argument('-d', '--dry', action='store_true', default=False, help='dry run') parser.add_argument('-v', '--verbose', action='store_true', default=False, help='verbose') args = parser.parse_args() for file in args.infile: eprint('Processing {}'.format(file.name)) lines = file.readlines() file.close() lines = remove_trailing_whitespace(lines) lines = fenced_code_blocks(lines) lines = headerlines_withspace(lines) lines = headerlines_surrounded(lines) #lines = long_lines(lines) if args.dry: eprint('Dry run: not writing file:\n-------------------------') print('\n'.join(lines)) else: # Make backup eprint('Writing {}'.format(file.name)) os.rename(file.name, file.name + '.bak') with open(file.name, 'w') as f: f.writelines('\n'.join(lines)) ","Python" "Bioengineering","telatin/seqfu2","test/test-rc.sh",".sh","1056","54","#!/bin/bash export SEQFU_QUIET=1 FOR=""CAGATA"" RC=""TATCTG"" OBS=$(""$BINDIR""/seqfu rc ""$FOR"") MSG=""Reverse complement of $FOR: exp=$RC got=$OBS"" if [[ $RC == $OBS ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi OBS=$(""$BINDIR""/seqfu rc ""$RC"") MSG=""Reverse complement of $RC: exp=$FOR got=$OBS"" if [[ $OBS == $FOR ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi #>polya #cagataaaaaaa #TTTTTTTATCTG OBS=$(""$BINDIR""/seqfu rc ""$FILES""/rc.fa | grep -v "">"") EXP=""TTTTTTTATCTG"" MSG=""Reverse complement of rc.fa: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ## IUPAC IUPAC=""ACGTWSKY"" EXP=""RMSWACGT"" OBS=$(""$BINDIR""/seqfu rc $IUPAC) MSG=""Reverse complement iupac $IUPAC: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-tabcheck.sh",".sh","1279","52","#!/bin/bash # Single file TABLE=""$FILES""/table-demo.tsv COMPR=""$FILES""/tablegz.tsv.gz WRONG=""$FILES""/table2.tsv for F in ""$TABLE"" ""$COMPR"" ""$WRONG""; do if [[ -e ""$F"" ]]; then echo -e ""$OK: Files exist: $F"" PASS=$((PASS+1)) else echo -e ""$FAIL: Files do not exist: $F"" ERRORS=$((ERRORS+1)) fi done # ----------------------------------------------------------------------------- EXP=1 MSG=""Check valid table"" OBS=$(""$BINDIR""/fu-tabcheck ""$TABLE"" | grep Pass | wc -l | grep -o '[[:digit:]]\+') if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi EXP=0 MSG=""Check wrong table"" OBS=$(""$BINDIR""/fu-tabcheck ""$WRONG"" | grep Pass | wc -l | grep -o '[[:digit:]]\+') if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi EXP=0 MSG=""Check details"" OBS=$(""$BINDIR""/fu-tabcheck ""$TABLE"" -i | grep Pass | wc -l | grep -o '[[:digit:]]\+') if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi","Shell" "Bioengineering","telatin/seqfu2","test/speed.sh",".sh","288","9","#!/bin/bash for FILE in /local/qi/import/AN/EG/Lcr/reads/7794_51_R1.fastq /local/qi/data/SC/CEL/reads/F09.fastq.gz ""$@""; do seqfu count ""$FILE"" BASE=$(basename ""$FILE"" | cut -f1 -d.) hyperfine ""./speed/native $FILE"" ""./speed/imported $FILE"" --export-markdown speed/""$BASE"".md done ","Shell" "Bioengineering","telatin/seqfu2","test/test-comp.sh",".sh","364","14","#!/bin/bash NATIVE=$(grep -v "">"" ""$FILES""/homopolymer.fa| wc -c) COMPRESSED=$(""$BINDIR""/fu-homocomp ""$FILES""/homopolymer.fa | grep -v "">"" | wc -c) if [[ $NATIVE -gt $COMPRESSED ]]; then echo -e ""$OK: compression from $NATIVE to $COMPRESSED"" PASS=$((PASS+1)) else echo -e ""$FAIL: compression from $NATIVE to $COMPRESSED"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-split.sh",".sh","3260","124","#!/bin/bash PY=$(command -v python) PYERR=$? if [[ -e ""$BINDIR""/fu-split ]] && [[ $PYERR == 0 ]]; then python --version export SEQFU_BIN=""$BINDIR""/seqfu # Single file OUTDIR=$(mktemp -d) echo "" * Outdir: $OUTDIR"" if [[ ! -d ""$OUTDIR"" ]]; then echo ""Error: output directory not created"" exit 1 fi touch ""$OUTDIR""/test.txt EXP=7 ""$BINDIR""/fu-split -i ""$i16S"" -n $EXP -o ""$OUTDIR""/splitParts-00000.fa.gz # -------------------------------------------------------------------------------- OBS=$(ls ""$OUTDIR""/splitParts-*.fa.gz | wc -l | grep -o '[[:digit:]]\+') MSG=""Split in $EXP files: got $OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ls -lh ""$OUTDIR""/splitParts-*.fa.gz ERRORS=$((ERRORS+1)) fi EXP=$(count ""$i16S"") OBS=$(""$BINDIR""/seqfu cat ""$OUTDIR""/splitParts-*.fa.gz | ""$BINDIR""/seqfu count | cut -f 2) MSG=""Total sequences from splitParts-*.fa.gz equal source: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi # Check total bases BASES=500000 ""$BINDIR""/fu-split -i ""$i16S"" -b $BASES -o ""$OUTDIR""/splitBases-00000.fa.gz # -------------------------------------------------------------------------------- EXP=$(bp ""$i16S"") OBS=$(bp ""$OUTDIR""/splitBases-*.fa.gz) MSG=""Split by $BASES bases: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi EXP=4 OBS=$(ls ""$OUTDIR""/splitBases-*.fa.gz | wc -l | grep -o '[[:digit:]]\+') MSG=""Split by bases: expecting $EXP files: got $OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ""$BINDIR""/seqfu stats -b -n ""$OUTDIR""/splitBases-*.fa.gz ERRORS=$((ERRORS+1)) fi # Each file should contain less than $BP bases for FILE in ""$OUTDIR""/splitBases*; do F=$(basename ""$FILE"") BP=$(bp ""$FILE"") if [[ ! $BP -gt $BASES ]]; then echo -e ""$OK: $F contains $BP bp: no more than $BASES"" PASS=$((PASS+1)) else echo -e ""$FAIL: $F contains $BP bp: more than $BASES"" ERRORS=$((ERRORS+1)) fi done # ============================================================================== # Check total seqs SEQS=1000 ""$BINDIR""/fu-split -i ""$i16S"" -s $SEQS -o ""$OUTDIR""/splitSeqs-00000.fa.gz # -------------------------------------------------------------------------------- EXP=$(bp ""$i16S"") OBS=$(bp ""$OUTDIR""/splitSeqs-*.fa.gz) MSG=""Split by $SEQS seqs: exp=$EXP got=$OBS "" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi # Each file should contain less than $SEQS sequences for FILE in ""$OUTDIR""/splitSeqs*; do COUNT=$(count ""$FILE"") F=$(basename ""$FILE"") if [[ ! $COUNT -gt $SEQS ]]; then echo -e ""$OK: $F contains $COUNT sequences: no more than $SEQS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $F contains $COUNT sequences: more than $SEQS"" ERRORS=$((ERRORS+1)) fi done if [[ $ERRORS == 0 ]]; then rm -rf ""$OUTDIR"" fi else echo -e ""SKIP: python not found ($PY) or fu-split not in $BINDIR"" fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-stats.sh",".sh","5419","194","#!/bin/bash # Single file TMP=$(mktemp) ""$BINDIR""/seqfu stats --basename ""$iAmpli"" > ""$TMP"" WC=$(cat ""$TMP"" | wc -l | grep -o '[[:digit:]]\+') SEQS=$(cat ""$TMP"" | tail -n 1 | cut -f 2) TOT=$(cat ""$TMP"" | tail -n 1 | cut -f 3) N50=$(cat ""$TMP"" | tail -n 1 | cut -f 5) MSG=""Checking normal output expecting 2 lines: <$WC>"" if [[ $WC == 2 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi MSG=""Checking normal output expecting total seqs 78730: <$SEQS>"" if [[ ""$SEQS"" == 78730 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi MSG=""Checking normal output expecting total bases 24299931: <$TOT>"" if [[ ""$TOT"" == 24299931 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi MSG=""Checking normal N50 to be 316: <$N50>"" if [[ $N50 == 316 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu stats --basename --csv ""$iAmpli"" > ""$TMP"" N50=$(cat ""$TMP"" | tail -n 1 | cut -f 5 -d ,) MSG=""Checking CSV output N50 is 316, got: <$N50>"" if [[ $N50 == 316 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi # Nice output ""$BINDIR""/seqfu stats --basename --nice ""$iAmpli"" > ""$TMP"" WC=$(cat ""$TMP"" | grep . | wc -l | grep -o '[[:digit:]]\+') if [[ ""$WC"" == 5 ]]; then echo -e ""$OK: Checking nice output expecting 5 lines: <$WC>"" PASS=$((PASS+1)) else echo -e ""$FAIL: Checking nice output expecting 5 lines: <$WC>"" ERRORS=$((ERRORS+1)) fi # Json TMP2=$(mktemp) ""$BINDIR""/seqfu stats --basename --json --multiqc ""$TMP2"" ""$iAmpli"" > ""$TMP"" WC=$(cat ""$TMP"" | grep . | wc -l | grep -o '[[:digit:]]\+') WC2=$(cat ""$TMP2"" | grep . | wc -l | grep -o '[[:digit:]]\+') if [[ ""$WC2"" == 39 ]]; then echo -e ""$OK: Checking MultiQC output expecting 39 lines: <$WC2>"" PASS=$((PASS+1)) else echo -e ""$FAIL: Checking MultiQC output expecting 39 lines: <$WC2>"" ERRORS=$((ERRORS+1)) fi if [[ $WC == 1 ]]; then echo -e ""$OK: Experimental JSON output on 1 line: <$WC>"" PASS=$((PASS+1)) else echo -e ""$FAIL: Experimental JSON output on 1 line: <$WC>"" ERRORS=$((ERRORS+1)) fi # Multi file # Default sort ""$BINDIR""/seqfu stats --basename ""$iAmpli"" ""$iSort"" ""$iMini"" > ""$TMP"" # Sort by N50 descending ""$BINDIR""/seqfu stats --basename --sort n50 --reverse ""$iAmpli"" ""$iSort"" ""$iMini"" > ""$TMP2"" FILT=$(cat ""$TMP"" | head -n 2 | tail -n 1 | cut -f 1) MSG=""Checking default starting by 'filt': <$FILT>"" if [[ ""$FILT"" == ""filt"" ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi FILT=$(cat ""$TMP2"" | head -n 2 |tail -n 1 | cut -f 1) MSG=""Checking default N50 starting by 'sort': <$FILT>"" if [[ ""$FILT"" == ""sort"" ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi #///// ""$BINDIR""/seqfu stats -a ""$FILES""/prot.faa ""$FILES""/prot2.faa ""$FILES""/test.fa ""$FILES""/test.fasta ""$FILES""/test.fastq ""$FILES""/test2.fastq ""$FILES""/test_4.fa.gz | grep -v ""Total bp"" > ""$TMP"" MSG=""Check absolute paths"" if [[ $(grep ^/ ""$TMP"" | cut -c 1 | sort | head -n 1 ) == ""/"" ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: "" ERRORS=$((ERRORS+1)) fi MSG=""Check sort orded when not specified"" A=$(basename $(head -n 1 ""$TMP"" | cut -f 1 ) ) if [[ ""$A"" == ""prot.faa"" ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: $A"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu stats -a --sort tot ""$FILES""/prot.faa ""$FILES""/prot2.faa ""$FILES""/test.fa ""$FILES""/test.fasta ""$FILES""/test.fastq ""$FILES""/test2.fastq ""$FILES""/test_4.fa.gz | grep -v ""Total bp"" > ""$TMP"" MSG=""Check sort: tot seq sorted at 3300"" if [[ $(head -n 1 ""$TMP"" | cut -f 3 ) == 3300 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG:$(head -n 1 ""$TMP"" | cut -f 3 ) "" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu stats -a --sort tot --reverse ""$FILES""/prot.faa ""$FILES""/prot2.faa ""$FILES""/test.fa ""$FILES""/test.fasta ""$FILES""/test.fastq ""$FILES""/test2.fastq ""$FILES""/test_4.fa.gz | grep -v ""Total bp"" > ""$TMP"" MSG=""Check reverse sort: tot seq sorted at 3300"" if [[ $(tail -n 1 ""$TMP"" | cut -f 3 ) == 3300 ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG:$(head -n 1 ""$TMP"" | cut -f 3 ) "" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu stats --gc ""$FILES""/gc/1.fa | grep -v ""Total bp"" > ""$TMP"" MSG=""%GC check at 1.00"" OUT=$(cut -f 11 ""$TMP"" ) if [[ ""$OUT"" == 1.00 ]]; then echo -e ""$OK: $MSG: <$OUT>"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG expected 1.00 got $OUT"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu stats --gc ""$FILES""/gc/2.fa | grep -v ""Total bp"" > ""$TMP"" MSG=""%GC check at 0.00"" OUT=$(cut -f 11 ""$TMP"" ) if [[ ""$OUT"" == 0.00 ]]; then echo -e ""$OK: $MSG: <$OUT>"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG expected 0.00 got $OUT"" ERRORS=$((ERRORS+1)) fi ""$BINDIR""/seqfu stats --gc ""$FILES""/gc/3.fa | grep -v ""Total bp"" > ""$TMP"" MSG=""%GC check at 0.50"" OUT=$(cut -f 11 ""$TMP"" ) if [[ ""$OUT"" == 0.50 ]]; then echo -e ""$OK: $MSG: <$OUT>"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG expected 0.50 got $OUT"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/mini.sh",".sh","11120","432","#!/bin/bash export SEQFU_QUIET=1 DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" BINDIR=""$DIR/../bin/"" BIN=""$BINDIR""/seqfu FILES=""$DIR""/../data/ iInterleaved=""$FILES""/interleaved.fq.gz iPair1=""$FILES""/illumina_1.fq.gz iPair2=""$FILES""/illumina_2.fq.gz iAmpli=""$FILES""/filt.fa.gz iSort=""$FILES""/sort.fa iMini=""$FILES""/target.fa i16S=""$FILES""/primers/16S_R1.fq.gz export iComments=""$FILES""/comments.fastq export iNum=""$FILES""/numbers.fa OK='\033[0;32mOK\033[0m' FAIL='\033[0;31mFAIL\033[0m' STAR='\033[1;34m->\033[0m' NOTE='\033[0;34m' BOLD='\033[1m' YELLOW='\033[1;33m' NC='\033[0m' ERRORS=0 getnumber() { echo ""$1"" | grep -o '[0-9]*' } count() { ""$BINDIR""/seqfu count ""$1"" | cut -f 2 } bp() { ""$BINDIR""/seqfu cat ""$@"" | ""$BINDIR""/seqfu stats | grep -v ""Total bp"" | cut -f 3 } function separator { # if length $1 > 0; then # echo -e ""\n$1\n"" if [[ $1 ]]; then echo -e ""${YELLOW}\033[1m $1 \033[0m"" fi DIV_BAR=""${YELLOW}\033[1m------------------------------------------------------------ \033[0m"" echo -e ""$DIV_BAR"" } separator ""Minimal test suite"" # Binary works ""$BIN"" > /dev/null || { echo ""Binary not working: $BIN""; exit 1; } echo -e ""$OK: Binary running"" BINCOUNT=0 for MOD in head tail view qual derep sort count stats grep rc interleave deinterleave count; do BINCOUNT=$((BINCOUNT+1)) echo -e "" $STAR $BINCOUNT. $MOD"" ""$BIN"" ""$MOD"" --help >/dev/null 2>&1 || { echo ""Help for $MOD returned non-zero""; exit 1; } done # Check version VERSION=$(""$BIN"" version) if [[ ""$VERSION"" == """" ]]; then echo ""Version not found"" ERRORS=$((ERRORS+1)) else grep ""$VERSION"" ""$DIR""/../seqfu.nimble fi PASS=0 ERRORS=0 # Dereiplicate if [[ $(""$BIN"" derep ""$iAmpli"" | grep -c '>') -eq ""18664"" ]]; then echo -e ""$OK: Dereplicate"" PASS=$((PASS+1)) else echo -e ""$FAIL: Dereplicate didnt return 18664 seqs"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" derep ""$iAmpli"" -m 10000 2>/dev/null | grep -c '>') -eq ""1"" ]]; then echo -e ""$OK: Dereplicate, min size"" PASS=$((PASS+1)) else echo -e ""$FAIL: Dereplicate, min size"" ERRORS=$((ERRORS+1)) fi # Grep if [[ $(""$BIN"" grep -n seq.1 ""$FILES""/comm.fa | grep -c '>') -eq ""1"" ]]; then echo -e ""$OK: grep, name"" PASS=$((PASS+1)) else echo -e ""$FAIL: grep, name"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" grep -c -n size=3 ""$FILES""/comm.fa | grep -c '>') -eq ""1"" ]]; then echo -e ""$OK: grep, size"" PASS=$((PASS+1)) else echo -e ""$FAIL: grep, size"" ERRORS=$((ERRORS+1)) fi # List if [[ $(""$BIN"" list ""$FILES""/prot.list ""$FILES""/prot.faa | grep -c '>') -eq ""5"" ]]; then echo -e ""$OK: list, default"" PASS=$((PASS+1)) else echo -e ""$FAIL: list, default not 5"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" list -c ""$FILES""/prot.list ""$FILES""/prot.faa | grep -c '>') -eq ""4"" ]]; then echo -e ""$OK: list, with comments"" PASS=$((PASS+1)) else echo -e ""$FAIL: list, with comments not 4"" ERRORS=$((ERRORS+1)) fi # Homopolymer HOMO=""$(dirname ""$BIN"")""/fu-homocomp if [[ -e ""$HOMO"" ]]; then ORIGINAL=$(grep . ""$FILES""/homopolymer.fq | wc -c | grep -o ""[[:digit:]]\+"") COMPRESSED=$($HOMO ""$FILES""/homopolymer.fq | wc -c | grep -o ""[[:digit:]]\+"") if [[ $ORIGINAL -gt $COMPRESSED ]]; then echo -e ""$OK: homopolymer pass $ORIGINAL > $COMPRESSED"" PASS=$((PASS+1)) else echo -e ""$FAIL: homopolymer failed $ORIGINAL original length, $COMPRESSED compressed length"" ERRORS=$((ERRORS+1)) fi fi # Interleave if [[ $(""$BIN"" ilv -1 ""$iPair1"" -2 ""$iPair2"" | wc -l) == $(cat ""$iPair1"" ""$iPair2"" | gzip -d | wc -l ) ]]; then echo -e ""$OK: Interleave"" PASS=$((PASS+1)) else echo -e ""$FAIL: Interleave differs cat/wc"" ERRORS=$((ERRORS+1)) fi # Deinterleave ""$BIN"" dei ""$iInterleaved"" -o testtmp if [[ $(grep . testtmp_R{1,2}.fq | wc -l) == $(gzip -dc ""$iInterleaved"" | wc -l ) ]]; then echo -e ""$OK: Deinterleave"" PASS=$((PASS+1)) else echo -e ""$FAIL: Deinterleave "" ERRORS=$((ERRORS+1)) fi rm testtmp_* # Count if [[ $(""$BIN"" count ""$iAmpli"" | cut -f 2) == $(gzip -dc ""$iAmpli"" | grep -c '>' ) ]]; then echo -e ""$OK: Count"" PASS=$((PASS+1)) else echo -e ""$FAIL: Count \""$BIN\"" count \""$iAmpli\"": differs grep/wc"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" count ""$iPair1"" ""$iPair2"" | wc -l) -eq 1 ]]; then echo -e ""$OK: Count pairs"" PASS=$((PASS+1)) else echo -e ""$FAIL: Count pairs"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" count -u ""$iPair1"" ""$iPair2"" | wc -l) -eq 2 ]]; then echo -e ""$OK: Count pairs, split"" PASS=$((PASS+1)) else echo -e ""$FAIL: Count pairs, split"" ERRORS=$((ERRORS+1)) fi ## Sort by size (asc) OUTPUT=$(""$BIN"" sort --asc ""$iSort"" | head -n 1| cut -c 2-6) if [[ $OUTPUT == 'short' ]]; then echo -e ""$OK: Sort by size"" PASS=$((PASS+1)) else echo -e ""$FAIL: Sort by size failed, exp short got '$OUTPUT'"" ERRORS=$((ERRORS+1)) fi ## Head if [[ $(""$BIN"" head -n 1 ""$iInterleaved"" | wc -l) -eq 4 ]]; then echo -e ""$OK: Head 1 sequence"" PASS=$((PASS+1)) else echo -e ""$FAIL: Head failed"" ERRORS=$((ERRORS+1)) fi ## Tail if [[ $(""$BIN"" tail -n 1 ""$iInterleaved"" | wc -l) -eq 4 ]]; then echo -e ""$OK: tail 1 sequence"" PASS=$((PASS+1)) else echo -e ""$FAIL: Tail failed"" ERRORS=$((ERRORS+1)) fi ##QUal if [[ $(""$BIN"" qual ""$iInterleaved"" | grep 'Illumina-1.8' | wc -l ) -eq 1 ]]; then echo -e ""$OK: qual tested"" PASS=$((PASS+1)) else echo -e ""$FAIL: qual failed"" ERRORS=$((ERRORS+1)) fi ## External # Seqfu ORF ORF1=$(""$BINDIR""/fu-orf -1 ""$iPair1"" -m 29 -r | grep -c '>') if [[ $ORF1 -eq 20 ]]; then echo -e ""$OK: fu-orf [-1] tested"" PASS=$((PASS+1)) else echo -e ""$FAIL: fu-orf [-1] test failed: $ORF1 != 20"" ERRORS=$((ERRORS+1)) fi ORFSE=$(""$BINDIR""/fu-orf ""$iPair1"" -m 29 -r | grep -c '>') if [[ $ORFSE -eq 20 ]]; then echo -e ""$OK: fu-orf [Single] tested"" PASS=$((PASS+1)) else echo -e ""$FAIL: fu-orf [Single] test failed: $ORFSE != 20"" ERRORS=$((ERRORS+1)) fi ORF2=$(""$BINDIR""/fu-orf -r -m 29 -1 ""$iPair1"" -2 ""$iPair2"" | grep -c '>') if [[ $ORF2 -gt 4 ]]; then echo -e ""$OK: fu-orf [Paired] tested"" PASS=$((PASS+1)) else echo -e ""$FAIL: fu-orf [Paired] test failed: $ORF2 != 5"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BINDIR""/fu-sw -q ""$FILES""/query.fa -t ""$FILES""/target.fa | grep -c -w '^Query') -eq 1 ]]; then echo -e ""$OK: fu-sw tested"" PASS=$((PASS+1)) else echo -e ""$FAIL: fu-sw header: test failed: != 1"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BINDIR""/fu-sw -q ""$FILES""/query.fa -t ""$FILES""/target.fa | grep -c '16S_') -eq 2 ]]; then echo -e ""$OK: fu-sw tested"" PASS=$((PASS+1)) else echo -e ""$FAIL: fu-sw alignments: test failed: != 2"" ERRORS=$((ERRORS+1)) fi ## STREAMING if [[ $( gzip -dc ""$iInterleaved"" | ""$BIN"" head -n 1 2>/dev/null | wc -l) -eq 4 ]]; then echo -e ""$OK: Head 1 sequence (stream)"" PASS=$((PASS+1)) else echo -e ""$FAIL: Head failed"" ERRORS=$((ERRORS+1)) fi if [[ $(gzip -dc ""$iInterleaved"" | ""$BIN"" tail -n 1 2>/dev/null | wc -l) -eq 4 ]]; then echo -e ""$OK: tail 1 sequence (stream)"" PASS=$((PASS+1)) else echo -e ""$FAIL: tail failed"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" head -n 6 ""$iInterleaved"" | ""$BIN"" tail -n 2 2>/dev/null | wc -l) -eq 8 ]]; then echo -e ""$OK: head/tail 1 sequence (stream)"" PASS=$((PASS+1)) else echo -e ""$FAIL: head/tail failed"" ERRORS=$((ERRORS+1)) fi # CAT if [[ $(""$BIN"" cat ""$iMini"" | head -n 1) == "">ecoli comment"" ]]; then echo -e ""$OK: cat: default"" PASS=$((PASS+1)) else echo -e ""$FAIL: cat: default"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" cat ""$iMini"" -s | head -n 1) == "">ecoli"" ]]; then echo -e ""$OK: cat: strip comment"" PASS=$((PASS+1)) else echo -e ""$FAIL: cat: strip comment"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" cat -z -p test_ ""$iMini"" | head -n 1) == "">test_1 comment"" ]]; then echo -e ""$OK: cat: prefix"" PASS=$((PASS+1)) else echo -e ""$FAIL: cat: prefix stripped didnt work: got $( ""$BIN"" cat -z -p test_ ""$iMini"" | head -n 1)"" ERRORS=$((ERRORS+1)) fi if [[ $(""$BIN"" cat -b ""$iMini"" -s | head -n 1) != "">target_ecoli"" ]]; then echo -e ""$FAIL: cat: basename not added"" ERRORS=$((ERRORS+1)) else echo -e ""$OK: cat: added basename"" PASS=$((PASS+1)) fi ## fu-cov TOTFILT=$(""$BINDIR""/fu-cov ""$FILES/ctgs.fa.gz"" -c 100 -x 200 2>/dev/null | grep -c '>') if [[ $((TOTFILT+0)) -eq 1 ]]; then echo -e ""$OK: fu-cov"" PASS=$((PASS+1)) else echo -e ""$FAIL: fu-cov was supposed to select 1 sequence, $TOTFILT found "" ERRORS=$((ERRORS+1)) fi echo """" SEARCH_DONE=0 for TEST in ""$DIR""/test-*.sh; do UTIL=$(basename ""$TEST"" | cut -f 1 -d '.' | cut -f 2 -d -) PREVPASS=$PASS PREVERR=$ERRORS if [[ $SEARCH_DONE -eq 1 ]]; then break fi if [[ ! -z ${1+x} ]] && [[ ""$1"" != ""$UTIL"" ]]; then echo Skipping $UTIL: looking for $1 continue fi if [[ -e $TEST ]]; then echo """" separator "" Testing module: $(basename ""$TEST"" .sh | cut -f 2 -d - )"" source ""$TEST"" if [[ $ERRORS -gt $PREVERR ]]; then echo -e ""$FAIL: Finished with $((PASS-PREVPASS)) passed, $((ERRORS-PREVERR)) failed"" else echo -e ""$NOTE# Finished with $((PASS-PREVPASS)) passed, $((ERRORS-PREVERR)) failed${NC}"" fi fi if [[ ! -z ${1+x} ]] && [[ ""$1"" == ""$UTIL"" ]]; then SEARCH_DONE=1 break fi done if [[ ! -z ${1+x} ]]; then exit 0 fi ## Check docs separator ""\n Checking docs"" for SUB in utilities tools; do echo "" - Utilities sort order in $SUB"" # Note: perl not installed in Github CI perl --version >/dev/null && grep ^sort: ""$DIR/../docs/$SUB/""[a-z]* | grep -v README | \ cut -f 2,3 -d : | \ sort | uniq -c | perl -mTerm::ANSIColor -ne ' if ($_=~/^\s*(\S)/) { if ($1 != ""1"") { print Term::ANSIColor::color(""red""), "" >>> RELEASE WARNING:"", Term::ANSIColor::color(""reset""), "" Wrong sort order: duplicate entry(es)\n""; die; } }' || grep ^sort: ""$DIR/../docs/$SUB/""[a-z]* | \ rev | \ sort -n | \ rev done ## Check release separator ""\n Checking release (GitHub)"" LOCAL_RELEASE=$(grep version ""$DIR/../seqfu.nimble"" | cut -f 2 -d = | sed 's/["" ]//g') GH_RELEASE=$(curl -s https://api.github.com/repos/telatin/seqfu2/releases/latest | perl -nE 'my ($tag, $val) = split /:/, $_; if ($tag=~/tag_name/) { my @tag = split /""/, $val; for my $i (@tag) { $i =~s/[^0-9.]//g; say $i if (length($i) > 2); } }') if [[ $LOCAL_RELEASE == $GH_RELEASE ]]; then echo "" ****************************************************************************"" echo "" Local $LOCAL_RELEASE matches remote $GH_RELEASE"" echo "" Set RELEASE=1 to make this warning fatal (e.g. when preparing a new release)"" echo "" ****************************************************************************"" echo if [[ $RELEASE == 1 ]]; then echo -e ""$FAIL: Release matches last version on GitHub"" ERRORS=$((ERRORS+1)) fi else echo -e ""$OK: Local Nimble release $LOCAL_RELEASE != $GH_RELEASE (remote)"" PASS=$((PASS+1)) fi echo "" Binary version $(""$BINDIR""/seqfu version)"" ### Check failures separator if [[ $ERRORS -gt 0 ]]; then echo -e ""$FAIL: $ERRORS test failed ($PASS passed)"" exit 1 else echo -e ""$OK: All $PASS tests passed"" fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-tofasta.sh",".sh","5662","176","#!/bin/bash export SEQFU_QUIET=1 TEMPFILENAME=$(mktemp) TOFASTA_DIR=""$FILES/tofasta"" # Test files CLUSTAL_FILE=""$TOFASTA_DIR/test.clw.gz"" GENBANK_FILE=""$TOFASTA_DIR/test.gbk.gz"" GFF_FILE=""$TOFASTA_DIR/test.gff.gz"" ### Test 1: Convert Clustal format ""$BINDIR""/seqfu tofasta ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.clw"" WC=$(grep -c '^>' ""$TEMPFILENAME.clw"") MSG=""tofasta: Clustal format conversion"" EXP=3 if [[ $EXP == $WC ]]; then echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" ERRORS=$((ERRORS+1)) fi ### Test 2: Convert GenBank format ""$BINDIR""/seqfu tofasta ""$GENBANK_FILE"" > ""$TEMPFILENAME.gbk"" WC=$(grep -c '^>' ""$TEMPFILENAME.gbk"") MSG=""tofasta: GenBank format conversion"" EXP=75 if [[ $EXP == $WC ]]; then echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" ERRORS=$((ERRORS+1)) fi ### Test 3: Convert GFF format ""$BINDIR""/seqfu tofasta ""$GFF_FILE"" > ""$TEMPFILENAME.gff"" 2>/dev/null WC=$(grep -c '^>' ""$TEMPFILENAME.gff"") MSG=""tofasta: GFF format conversion"" EXP=226 if [[ $EXP == $WC ]]; then echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" ERRORS=$((ERRORS+1)) fi ### Test 4: Uppercase transformation ""$BINDIR""/seqfu tofasta -u ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.upper"" # Check if sequences are uppercase (should not contain lowercase letters) LOWERCASE_COUNT=$(grep -v '^>' ""$TEMPFILENAME.upper"" | grep -o '[a-z]' | wc -l | tr -d ' ') MSG=""tofasta: uppercase transformation"" EXP=0 if [[ $EXP == $LOWERCASE_COUNT ]]; then echo -e ""$OK: $MSG (no lowercase letters found)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (found $LOWERCASE_COUNT lowercase letters, expected 0)"" ERRORS=$((ERRORS+1)) fi ### Test 5: Lowercase transformation ""$BINDIR""/seqfu tofasta -l ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.lower"" # Check if sequences are lowercase (should not contain uppercase letters) UPPERCASE_COUNT=$(grep -v '^>' ""$TEMPFILENAME.lower"" | grep -o '[A-Z]' | wc -l | tr -d ' ') MSG=""tofasta: lowercase transformation"" EXP=0 if [[ $EXP == $UPPERCASE_COUNT ]]; then echo -e ""$OK: $MSG (no uppercase letters found)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (found $UPPERCASE_COUNT uppercase letters, expected 0)"" ERRORS=$((ERRORS+1)) fi ### Test 6: Replace IUPAC ambiguous bases ""$BINDIR""/seqfu tofasta -n ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.iupac"" # Check if R (in gene01: ATGCRAGGAT) was replaced with N R_COUNT=$(grep -v '^>' ""$TEMPFILENAME.iupac"" | grep -o 'R' | wc -l | tr -d ' ') MSG=""tofasta: replace non-IUPAC with N"" EXP=0 if [[ $EXP == $R_COUNT ]]; then echo -e ""$OK: $MSG (R was replaced)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (found $R_COUNT 'R' characters, expected 0)"" ERRORS=$((ERRORS+1)) fi ### Test 7: Multiple files with output file ""$BINDIR""/seqfu tofasta -o ""$TEMPFILENAME.multi"" ""$CLUSTAL_FILE"" ""$GENBANK_FILE"" 2>/dev/null if [[ -f ""$TEMPFILENAME.multi"" ]]; then WC=$(grep -c '^>' ""$TEMPFILENAME.multi"") MSG=""tofasta: multiple files to output file"" EXP=78 # 3 from Clustal + 75 from GenBank if [[ $EXP == $WC ]]; then echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" ERRORS=$((ERRORS+1)) fi else echo -e ""$FAIL: tofasta: output file was not created"" ERRORS=$((ERRORS+1)) fi ### Test 8: Verbose mode stderr output VERBOSE_OUTPUT=$(""$BINDIR""/seqfu tofasta -v ""$CLUSTAL_FILE"" 2>&1 >/dev/null) if echo ""$VERBOSE_OUTPUT"" | grep -q ""Format: Clustal""; then echo -e ""$OK: tofasta: verbose mode works"" PASS=$((PASS+1)) else echo -e ""$FAIL: tofasta: verbose mode did not print format"" ERRORS=$((ERRORS+1)) fi ### Test 9: Check sequence correctness (GenBank ID) GB_HEADER=$(head -n 1 ""$TEMPFILENAME.gbk"") if echo ""$GB_HEADER"" | grep -q ""NZ_AHMY02000075""; then echo -e ""$OK: tofasta: GenBank sequence ID correct"" PASS=$((PASS+1)) else echo -e ""$FAIL: tofasta: GenBank sequence ID not found (got: $GB_HEADER)"" ERRORS=$((ERRORS+1)) fi ### Test 10: Check sequence correctness (Clustal IDs) GENE01_FOUND=$(grep -c '^>gene01' ""$TEMPFILENAME.clw"") GENE02_FOUND=$(grep -c '^>gene02' ""$TEMPFILENAME.clw"") GENE03_FOUND=$(grep -c '^>gene03' ""$TEMPFILENAME.clw"") MSG=""tofasta: Clustal sequence IDs correct"" if [[ $GENE01_FOUND == 1 ]] && [[ $GENE02_FOUND == 1 ]] && [[ $GENE03_FOUND == 1 ]]; then echo -e ""$OK: $MSG (all 3 genes found)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (gene01=$GENE01_FOUND, gene02=$GENE02_FOUND, gene03=$GENE03_FOUND)"" ERRORS=$((ERRORS+1)) fi ### Test 11: Sequence content preservation (check gaps were removed) # Clustal alignment has gaps (-), FASTA output should not GAP_COUNT=$(grep -v '^>' ""$TEMPFILENAME.clw"" | grep -o '\-' | wc -l | tr -d ' ') MSG=""tofasta: gaps preserved in output"" # We expect gaps to be preserved in the sequence (they are valid FASTA characters) if [[ $GAP_COUNT -gt 0 ]]; then echo -e ""$OK: $MSG (found $GAP_COUNT gaps as expected)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (no gaps found, expected some)"" ERRORS=$((ERRORS+1)) fi ### Test 12: Help text if ""$BINDIR""/seqfu tofasta --help 2>&1 | grep -q ""Convert various sequence formats""; then echo -e ""$OK: tofasta: help text available"" PASS=$((PASS+1)) else echo -e ""$FAIL: tofasta: help text not found"" ERRORS=$((ERRORS+1)) fi # Cleanup rm -f ""$TEMPFILENAME""* ","Shell" "Bioengineering","telatin/seqfu2","test/deinterleave.md",".md","2795","88","# Reference deinterleave.sh script ```bash #!/bin/bash DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" PLATFORM="""" if [[ $(uname) == ""Darwin"" ]]; then PLATFORM="""" fi BIN=$DIR/../bin/seqfu${PLATFORM} FILES=$DIR/../data/ # Files iInterleaved=$FILES/interleaved.fq.gz iInterleavedFQ=$FILES/tests/interleavedFQ.fq iInterUNEVEN=$FILES/tests/unevenInterleaved.fq iInterLONG1=$FILES/tests/longerone.fq iInterLONG2=$FILES/tests/longertwo.fq iAllEMPTY=$FILES/tests/empty.fq iAllMISS=$FILES/tests/nonexistent.fq ERRORS=0 echo ""# Testing -deinterleave- function"" # Binary works $BIN > /dev/null|| { echo ""Binary not working""; exit 1; } echo ""OK: Running"" # Deinterleave normal gzipped echo """" echo ""1. TEST - de-interleave a gzipped fastq file"" echo ""COMMAND: $BIN dei -v -o testtmp $iInterleaved"" $BIN dei -v -o testtmp $iInterleaved if [[ $(cat testtmp_R1.fq testtmp_R2.fq | wc -l) == $(cat $iInterleaved | gunzip | wc -l ) ]]; then echo ""OK: Deinterleave gzipped fastq"" else echo ""ERR: Deinterleave gzipped fastq"" ERRORS=$((ERRORS+1)) fi # Deinterleave normal echo """" echo ""2. TEST - de-interleave a fastq file"" echo ""COMMAND: $BIN dei -v -o testtmpFQ $iInterleavedFQ"" $BIN dei -v -o testtmpFQ $iInterleavedFQ if [[ $(cat testtmpFQ_R1.fq testtmpFQ_R2.fq | wc -l) == $(cat $iInterleavedFQ | wc -l ) ]]; then echo ""OK: Deinterleave fastq"" else echo ""ERR: Deinterleave fastq"" ERRORS=$((ERRORS+1)) fi # Deinterleave normal other extension echo """" echo ""3. TEST - de-interleave a fastq file into custom extension"" echo ""COMMAND: $BIN dei -v -f _forward.fq -r _reverse.fq -o testtmpcus $iInterleaved"" $BIN dei -v -f _forward.fq -r _reverse.fq -o testtmpcus $iInterleaved if [[ $(cat testtmpcus_forward.fq testtmpcus_reverse.fq | wc -l) == $(cat $iInterleaved | gunzip | wc -l ) ]]; then echo ""OK: Deinterleave fastq custom extension"" else echo ""ERR: Deinterleave fastq custom extension"" ERRORS=$((ERRORS+1)) fi # Deinterleave uneven fastq # needed: warning if more reads of either R1 or R2 echo """" echo ""4. TEST - de-interleave a fastq file with uneven number of reads"" echo ""COMMAND: $BIN dei -v -o testtmpuneven $iInterUNEVEN"" $BIN dei -v -o testtmpuneven $iInterUNEVEN # Deinterleave empty fastq # needed: warning if input file is empty ""no sequenes in file X""; at the moment: produces empty R1 and R2 but no warning #echo """" #echo ""5. TEST - de-interleave empty fastq file"" #echo ""COMMAND: $BIN dei -v -o testtmpempty $iAllEMPTY"" #$BIN dei -v -o testtmpempty $iAllEMPTY # Deinterleave nonexistent # needed: warning if input file is nonexistent; at the moment: error #echo """" #echo ""6. TEST - de-interleave a non-existent fastq file"" #echo ""COMMAND: $BIN dei -v -o testtmpmiss $iAllMISS"" #$BIN dei -v -o testtmpmiss $iAllMISS rm testtmp* ```","Markdown" "Bioengineering","telatin/seqfu2","test/test-split_nozip.sh",".sh","2902","120","#!/bin/bash PY=$(command -v python) if [[ -e ""$BINDIR""/fu-split ]] && [[ $PYERR == 0 ]]; then python --version # Single file OUTDIR=$(mktemp -d) if [[ ! -d ""$OUTDIR"" ]]; then echo ""Error: output directory not created"" exit 1 fi touch ""$OUTDIR""/test.txt EXP=7 ""$BINDIR""/fu-split -i ""$i16S"" -n $EXP -o ""$OUTDIR""/splitParts-00000.fa OBS=$(ls ""$OUTDIR""/splitParts-*.fa | wc -l | grep -o '[[:digit:]]\+') MSG=""Split in $EXP files: got $OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ls -lh ""$OUTDIR""/splitParts-*.fa ERRORS=$((ERRORS+1)) fi EXP=$(count ""$i16S"") OBS=$(""$BINDIR""/seqfu cat ""$OUTDIR""/splitParts-*.fa | ""$BINDIR""/seqfu count | cut -f 2) MSG=""Total sequences from splitParts-*.fa equal source: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi # Check total bases BASES=500000 ""$BINDIR""/fu-split -i ""$i16S"" -b $BASES -o ""$OUTDIR""/splitBases-00000.fa EXP=$(bp ""$i16S"") OBS=$(bp ""$OUTDIR""/splitBases-*.fa) MSG=""Split by $BASES bases: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi EXP=4 OBS=$(ls ""$OUTDIR""/splitBases-*.fa | wc -l | grep -o '[[:digit:]]\+') MSG=""Split by bases in $EXP files: got $OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ""$BINDIR""/seqfu stats -b -n ""$OUTDIR""/splitBases-*.fa ERRORS=$((ERRORS+1)) fi # Each file should contain less than $BP bases for FILE in ""$OUTDIR""/splitBases*; do F=$(basename ""$FILE"") BP=$(bp ""$FILE"") if [[ ! $BP -gt $BASES ]]; then echo -e ""$OK: $F contains $BP bp: no more than $BASES"" PASS=$((PASS+1)) else echo -e ""$FAIL: $F contains $BP bp: more than $BASES"" ERRORS=$((ERRORS+1)) fi done # ============================================================================== # Check total seqs SEQS=1000 ""$BINDIR""/fu-split -i ""$i16S"" -s $SEQS -o ""$OUTDIR""/splitSeqs-00000.fa EXP=$(bp ""$i16S"") OBS=$(bp ""$OUTDIR""/splitSeqs-*.fa) MSG=""Split by $SEQS seqs: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi # Each file should contain less than $SEQS sequences for FILE in ""$OUTDIR""/splitSeqs*; do COUNT=$(count ""$FILE"") F=$(basename ""$FILE"") if [[ ! $COUNT -gt $SEQS ]]; then echo -e ""$OK: $F contains $COUNT sequences: no more than $SEQS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $F contains $COUNT sequences: more than $SEQS"" ERRORS=$((ERRORS+1)) fi done if [[ $ERRORS == 0 ]] then rm -rf ""$OUTDIR"" fi else echo -e ""SKIP: python not found ($PY) or fu-split not in $BINDIR"" fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-check.sh",".sh","8056","311"," #!/bin/bash export SEQFU_QUIET=1 TEMPFILENAME=$(mktemp) ### SINGLE END ""$BINDIR""/seqfu check ""$FILES""/illumina_nocomm.fq > ""$TEMPFILENAME"" IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) EXIT=$? MSG=""Checked single end exit status"" EXP=0 if [[ $EXIT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $EXIT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $EXIT)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked single end OK"" EXP=1 if [[ $IS_OK == ""$EXP"" ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked single end libtype"" EXP=""SE"" if [[ $LIBRARY == ""$EXP"" ]]; then echo -e ""$OK: $MSG (expected $EXP, got $LIBRARY)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $LIBRARY)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked single end sequence count"" EXP=7 if [[ $COUNT == ""$EXP"" ]]; then echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" ERRORS=$((ERRORS+1)) fi ### BAD SE, SINGLE END, DEEP ""$BINDIR""/seqfu check --deep ""$FILES""/bad.fastq > ""$TEMPFILENAME"" IS_OK=$(grep -c ""ERR"" ""$TEMPFILENAME"" ) COUNT=$(cut -f 4 ""$TEMPFILENAME"") LIBRARY=$(cut -f 2 ""$TEMPFILENAME"" ) EXIT=$? MSG=""Checked BAD single end exit status with --deep"" EXP=1 if [[ $IS_OK == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi MSG=""Counts checking BAD single end exit status with --deep"" EXP=0 if [[ $COUNT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi ### BAD PE, DEEP ""$BINDIR""/seqfu check --deep --dir ""$FILES""/check/pe/ > ""$TEMPFILENAME"" IS_OK=$(grep -c ""ERR"" ""$TEMPFILENAME"" ) COUNT=$(cut -f 4 ""$TEMPFILENAME"" | awk '{ sum += $1 } END { print sum }') LIBRARY=$(cut -f 2 ""$TEMPFILENAME"" ) EXIT=$? MSG=""Checked BAD paired end exit status with --deep"" EXP=2 if [[ $IS_OK == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi MSG=""Counts checking BAD paired end exit status with --deep"" EXP=0 if [[ $COUNT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" ERRORS=$((ERRORS+1)) fi ### BAD SE, SINGLE END, NO DEEP ""$BINDIR""/seqfu check ""$FILES""/bad.fastq > ""$TEMPFILENAME"" IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) EXIT=$? MSG=""Checked BAD single end exit status without --deep"" EXP=1 if [[ $IS_OK == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi MSG=""Counts checking BAD single end exit status without --deep"" EXP=0 if [[ $COUNT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi ### PAIRED END ""$BINDIR""/seqfu check ""$FILES""/illumina_1.fq.gz > ""$TEMPFILENAME"" EXIT=$? IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) MSG=""Checked paired end"" EXP=1 if [[ $IS_OK == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked paired end exit status"" EXP=0 if [[ $EXIT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $EXIT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $EXIT)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked paired end libtype"" EXP=""PE"" if [[ $LIBRARY == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $LIBRARY)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $LIBRARY)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked single end sequence count (2xSE)"" EXP=14 if [[ $COUNT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" ERRORS=$((ERRORS+1)) fi ## INVALID PE ""$BINDIR""/seqfu check ""$FILES""/longerone_R1.fq.gz > ""$TEMPFILENAME"" EXIT=$? IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) MSG=""Checked INVALID paired end"" EXP=0 if [[ $IS_OK == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked INVALID paired end exit status"" EXP=0 if [[ $EXIT -gt $EXP ]]; then echo -e ""$OK: $MSG (got $EXIT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (got $EXIT)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked INVALID paired end libtype"" EXP=""PE"" if [[ $LIBRARY == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $LIBRARY)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $LIBRARY)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked INVALID paired end sequence count (2xSE)"" EXP=""-"" if [[ $COUNT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" ERRORS=$((ERRORS+1)) fi ### CHECK INVALID DIR LSDIR=$(ls -lh ""$FILES""/primers) $BINDIR/seqfu check --verbose --dir ""$FILES/primers"" > ""$TEMPFILENAME"" 2> ""$TEMPFILENAME.log"" EXIT=$? WC=$(getnumber $(cat ""$TEMPFILENAME"" | wc -l)) WC_ERR=$(getnumber $(cat ""$TEMPFILENAME"" | grep -v OK | grep ERR | wc -l)) MSG=""Checked INVALID directory ($FILES/primers) exit status"" if [[ $EXIT -gt 0 ]]; then echo -e ""$OK: $MSG (expected > 0, got $EXIT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected > 0, got $EXIT)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked INVALID directory line count"" EXP=14 if [[ $WC == $EXP ]]; then echo -e ""$OK: $MSG (got $WC expected $EXP)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (got $WC expected $EXP)\n$(cat ""$TEMPFILENAME"")\n$LSDIR"" ERRORS=$((ERRORS+1)) fi MSG=""Checked INVALID directory line error count"" EXP=2 if [[ $WC_ERR == $EXP ]]; then echo -e ""$OK: $MSG (got $WC_ERR expected $EXP)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (got $WC_ERR expected $EXP)\n$(cat ""$TEMPFILENAME"")\n$LSDIR"" ERRORS=$((ERRORS+1)) fi ### CHECK VALID DIR: WHICH ONE? TMP_CHECK_DIR_VALID=$(mktemp -d SEQFU_TMPDIR_XXXXXX) cp ""$FILES""/illumina_{1,2}.fq.gz ""$TMP_CHECK_DIR_VALID""/ ""$BINDIR""/seqfu check --verbose --dir ""$TMP_CHECK_DIR_VALID"" > ""$TMP_CHECK_DIR_VALID/out"" 2> ""$TMP_CHECK_DIR_VALID/log"" EXIT=$? WC=$(getnumber ""$( wc -l < ""$TMP_CHECK_DIR_VALID/out"")"" ) WC_ERR=$(getnumber ""$( grep -v OK ""$TMP_CHECK_DIR_VALID/out"" | grep -c ""ERR"")"" ) rm -rf ""$TMP_CHECK_DIR_VALID"" MSG=""Checked valid directory $TMP_CHECK_DIR_VALID exit status"" if [[ $EXIT -eq 0 ]]; then echo -e ""$OK: $MSG (expected 0, got $EXIT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected 0, got $EXIT)\n"" ERRORS=$((ERRORS+1)) fi MSG=""Checked valid directory line count $TMP_CHECK_DIR_VALID/out"" EXP=1 if [[ ""$WC"" == ""$EXP"" ]]; then echo -e ""$OK: $MSG (got $WC expected $EXP)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (got $WC expected $EXP)"" ERRORS=$((ERRORS+1)) fi MSG=""Checked valid directory line error count"" EXP=0 if [[ $WC_ERR == $EXP ]]; then echo -e ""$OK: $MSG (got $WC_ERR expected $EXP)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (got $WC_ERR expected $EXP)"" ERRORS=$((ERRORS+1)) fi rm ""$TEMPFILENAME""","Shell" "Bioengineering","telatin/seqfu2","test/test-grep.sh",".sh","4635","173","#!/bin/bash # Single file TMP=$(mktemp) echo "" Temp file: $TMP"" ## Get SEQ3 EXP=1 MSG=""Extracting one exact match (SEQ3)"" OBS=$(""$BINDIR""/seqfu grep -n SEQ3 ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Get SEQ3 (-v) EXP=4 MSG=""Extracting one exact match (SEQ3), invert (-v)"" OBS=$(""$BINDIR""/seqfu grep -v -n SEQ3 ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Get SEQ EXP=5 MSG=""Get all SEQ matches"" OBS=$(""$BINDIR""/seqfu grep -n SEQ ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Get seq *none* EXP=0 MSG=""Extracting all 'seq' matches"" OBS=$(""$BINDIR""/seqfu grep -n seq ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Get seq *none* EXP=5 MSG=""Extracting all 'seq' matches, but case insensitive"" OBS=$(""$BINDIR""/seqfu grep -i -n seq ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Get seq with regex EXP=10 MSG=""Regex '1.3' matches (-r)"" OBS=$(""$BINDIR""/seqfu grep -r 1.3 ""$iNum"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Get seq full EXP=1 MSG=""Full '13' matches (-f)"" OBS=$(""$BINDIR""/seqfu grep -n 13 -f ""$iNum"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Search patter EXP=0 MSG=""Search 'two' (is only in comments)"" OBS=$(""$BINDIR""/seqfu grep -n two ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Search in comments EXP=3 MSG=""Search 'two' (INCLUDING comments)"" OBS=$(""$BINDIR""/seqfu grep -c -n two ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ## Search oligo EXP=1 MSG=""Search oligo"" OBS=$(""$BINDIR""/seqfu grep -o ACGTACGTACGTAGCTGATCGATCGTACGTAGCTGACA ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi EXP=1 MSG=""Search oligo, revcompl and lowercase"" OBS=$(""$BINDIR""/seqfu grep -o tgtcagctacgtacgatcgatcagctacgtacgtacgt ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi EXP=1 MSG=""Search oligo (lower case in UC seq)"" OBS=$(""$BINDIR""/seqfu grep -o acgtacgtacgtagctgatcgatcgtacgtagctgaca ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi EXP=1 MSG=""Search oligo (partial with 'N' inside)"" OBS=$(""$BINDIR""/seqfu grep -o tacgtacgtagctgatcNatcgtacgtagctgaca ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi EXP=1 MSG=""Search oligo (partial with 'IUPAC' inside)"" OBS=$(""$BINDIR""/seqfu grep -o acgtacgtacgtaSStgatcgatcgtacgtagctgaca ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) if [[ $OBS -eq $EXP ]]; then echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/test-tail.sh",".sh","572","31","#!/bin/bash export SEQFU_QUIET=1 TMP=$(mktemp) $(""$BINDIR""/seqfu tail ""$iNum"" > ""$TMP"") OBS=$(count ""$TMP"") EXP=10 MSG=""Last seqs (default) $TMP: exp=$EXP got=$OBS"" if [[ $EXP == $OBS ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi EXP=50 $(""$BINDIR""/seqfu tail -n $EXP ""$iNum"" > ""$TMP"") OBS=$(count ""$TMP"") MSG=""Last '-n $EXP' seqs $TMP: exp=$EXP got=$OBS"" if [[ $EXP == $OBS ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi rm ""$TMP"" ","Shell" "Bioengineering","telatin/seqfu2","test/makezip.sh",".sh","944","39","#!/bin/bash set -euxo pipefail check_gh() { # Check if `gh` command is available if command -v gh >/dev/null 2>&1; then echo ""OK: GitHub CLI 'gh' found"" gh --version return 0 else echo ""ERROR: GitHub CLI 'gh' was not found"" echo ""Please install it from https://cli.github.com/"" return 1 fi } getversion() { new_tag=""v$(grep version ""$DIR""/../seqfu.nimble | cut -f 2 -d \"")"" # check if gh() if check_gh; then new_tag=$(gh release list -L 1 | grep -o ""v\d\+\.\d\+\.\d\+"") else echo ""Could not get remote release"" fi } DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" BINDIR=""$DIR""/../bin/ DESTDIR=""$DIR""/../releases/zips/ programName=""SeqFu"" os_tag=""$(uname -s)-$(uname -m)"" new_tag=""unknown"" getversion mkdir -p ""$DESTDIR"" ZIP=""$DESTDIR""/${programName}-${new_tag}-${os_tag}.zip zip -j ""$ZIP"" ""$BINDIR""/* gh release upload ${new_tag} ""$ZIP"" ","Shell" "Bioengineering","telatin/seqfu2","test/screenshot.sh",".sh","644","26","#!/usr/bin/env bash # Automate screeshots with termshot # Check if termshot is available if ! command -v termshot &> /dev/null then echo ""termshot could not be found"" echo ""Install it with:"" echo ""brew install homeport/tap/termshot"" exit fi echo ""termshot found, continuing..."" make echo ""Setting up test environment..."" export PATH=$PWD/bin:$PATH for PROG in cat count deinterleave derep grep head interleave lanes metadata rc rotate stats tab tail; do termshot --show-cmd --filename docs/img/screenshot-${PROG}.png -- seqfu $PROG --help done termshot --show-cmd --filename docs/img/screenshot-seqfu.png -- seqfu ","Shell" "Bioengineering","telatin/seqfu2","test/release.py",".py","8435","296","#!/usr/bin/env python3 """""" LOCAL_RELEASE=$(cat ""$DIR/../seqfu.nimble"" | grep version | cut -f 2 -d = | sed 's/["" ]//g') GH_RELEASE=$(curl -s https://api.github.com/repos/telatin/seqfu2/releases/latest | perl -nE 'my ($tag, $val) = split /:/, $_; if ($tag=~/tag_name/) { my @tag = split /""/, $val; for my $i (@tag) { $i =~s/[^0-9.]//g; say $i if (length($i) > 2); } }') """""" import subprocess import sys import json import urllib.request import os import re import hashlib programName='SeqFu' def eprint(*args, **kwargs): # import sys print(*args, file=sys.stderr, **kwargs) def jsonFromURL(uri): operUrl = urllib.request.urlopen(uri) if(operUrl.getcode()==200): data = operUrl.read() jsonData = json.loads(data) else: eprint(""Error receiving data"", operUrl.getcode()) return jsonData def get_os(): arch = subprocess.getoutput(['uname -m']) machine = subprocess.getoutput(['uname -s']) return machine + '-' + arch def check_gh(): command = ['gh', 'version'] expected_return_code = 0 try: result = subprocess.run(command, stdout=subprocess.PIPE) if result.returncode == expected_return_code: return True else: return False except Exception as e: eprint(f""WARNING: checking `gh` failed:\n{e}."") return False def get_last_release(): """""" Retrieve the last release tag from Github """""" releaseInfo = jsonFromURL('https://api.github.com/repos/telatin/seqfu2/releases/latest') if 'tag_name' in releaseInfo: return releaseInfo['tag_name'] else: eprint(""ERROR: Unable to get the last release"") quit(1) def get_curr_release(file): """""" Extract the last version from Nimble """""" try: with open(file, 'r') as fd: content = fd.read() match = re.search('version\s+=\s+""(.+?)""', content) if match.group(1) is not None: return match.group(1) else: eprint(f""WARNING: Version not found in {file}"") return """" except Exception as e: eprint(f""ERROR loading {file}:\n{e}"") quit(1) def get_output(bin): result = subprocess.run([bin], stdout=subprocess.PIPE) return result.stdout.decode(""utf-8"") def md5sum(rootdir, filename, blocksize=2**20): m = hashlib.md5() with open( os.path.join(rootdir, filename) , ""rb"" ) as f: while True: buf = f.read(blocksize) if not buf: break m.update( buf ) return m.hexdigest() def list_files_md(bindir): """""" list files in a directory """""" files = os.listdir(bindir) md = """" list = {} for f in files: if f == 'seqfu': continue help_page = f""{bindir}/../docs/utilities/{f}.md"" md5 = md5sum(bindir, f) list[f] = md5 if not os.path.exists(help_page): eprint(f""WARNING: {help_page} not found"") md += f"" * {f}\n"" else: md += "" * ["" + f + ""]({{site.baseurl}}/utilities/"" + f + "".html)\n"" return [md, list] def get_core_utils(dir): md = """" for file in os.listdir(dir): module = file.split(""."") md += f"" * [seqfu {module[0]}]("" + ""{{site.baseurl}}/tools/"" + module[0] + "".html)\n"" return md def init_markdown(file, release, changes, bindir): """""" create an empty markdown page """""" splash = get_output(f""{bindir}/seqfu"") core = get_core_utils(f""{bindir}/../docs/tools/"") #changes = """" utils, data = list_files_md(bindir) template = f""""""# {programName} {release} ### Changes {changes} ### Splash screen ```text {splash} ``` """""" try: with open(file, 'w') as f: print(template, file=f) except Exception as e: eprint(f""ERROR trying to write MD file to {file}:\n{e}"") def print_as_json(data, file): try: with open(file, 'w+') as fp: fp.write(json.dumps(data)) except Exception as e: eprint(f""ERROR: Unable to print JSON to {file}:\n{e}"") quit(1) if __name__ == ""__main__"": import argparse parser = argparse.ArgumentParser(description=f'Release a new version of {programName}') parser.add_argument(""-s"", ""--skip-build"", help=""Skip build step"", action=""store_true"") parser.add_argument(""-D"", ""--delete"", help=""delete the readme file"", action=""store_true"") parser.add_argument(""-x"", ""--skip-test"", help="""", action=""store_true"") parser.add_argument(""-v"", ""--verbose"", help=""Enable verbose output"", action=""store_true"") parser.add_argument(""-r"", ""--release"", help=""Make release"", action=""store_true"") args = parser.parse_args() if not check_gh(): eprint(""ERROR: `gh` is required."") quit(1) # Relevant variables last_release = get_last_release() script_dir = os.path.dirname(os.path.realpath(__file__)) curr_release = get_curr_release(f""{script_dir}/../{programName.lower()}.nimble"") basedir = f""{script_dir}/../"" bindir = f""{basedir}/bin/"" bin = f""{bindir}/seqfu"" new_tag = f""v{curr_release}"" changelog = f""{basedir}/releases/changes.md"" os_tag = get_os() release_text = """" try: with open(changelog) as ch: release_text = ch.read() except Exception as e: eprint(f""ERROR: Change log not found {changelog}.\n{e}"") quit(1) if len(release_text) == 0: eprint(""No release notes"") quit(1) if args.verbose: eprint(f""Last GH release:\t{last_release}"") eprint(f""Current release:\t{new_tag}"") eprint(f""Platform: \t{os_tag}"") # Build if not args.skip_build: os.chdir(f""{script_dir}/.."") for f in os.listdir(f""{script_dir}/../bin/""): path = os.path.join(f""{script_dir}/../bin"", f) eprint(f""Removing {path}"") os.remove(path) build = subprocess.run(['nimble', 'build']) if build.returncode != 0: eprint(""Build failed."") quit(1) # Test if not args.skip_test: subprocess.run(['bash', f'{script_dir}/../test/mini.sh']) release_notes = f""{script_dir}/../docs/releases/{new_tag}.md"" release_dir = f""{basedir}/releases/"" # Make directory ${release_dir}/zips if not exists zip_dir = os.path.join(release_dir, ""zips"") if not os.path.exists(zip_dir): os.makedirs(zip_dir) # Prepare zip zipfile = f""{release_dir}/zips/{programName}-{new_tag}-{os_tag}.zip"" binaries = ['zip', '-q', '-j', zipfile] for file in os.listdir(bindir): binaries.append(os.path.join(bindir, file)) eprint(f""Making zip file: {zipfile}"") subprocess.run(binaries) # Check that there's a new release if last_release == new_tag: eprint(f""ERROR: Update the release first: {new_tag} already published"") quit(1) # Prepare release dir eprint(f""Release dir: {release_dir}"") # Prepare splash screen archive # CORE splashes = {} try: for coreManPage in os.listdir(f""{basedir}/docs/tools/""): if coreManPage == 'README.md': continue core = coreManPage.split('.')[0] splash = subprocess.run([f'{bindir}/seqfu', core, '--help'], stdout=subprocess.PIPE) splash_screen = splash.stdout.decode('utf-8') splashes[f""seqfu {core}""] = splash_screen except Exception as e: quit() # UTILS: try: for utilManPage in os.listdir(f""{basedir}/docs/utilities/""): if utilManPage == 'README.md': continue core = utilManPage.split('.')[0] eprint([core, '--help']) splash = subprocess.run([f'{bindir}/{core}', '--help'], stdout=subprocess.PIPE) splash_screen = splash.stdout.decode('utf-8') splashes[core] = splash_screen except Exception as e: eprint(f""Error in {utilManPage}: {e}"") quit() #print_as_json(splashes, os.path.join(release_dir, f""{new_tag}.splashes.json"")) # Generate new release document if False:# and not os.path.exists(release_notes) or args.delete: eprint(f""Generating new page: {release_notes}"") splash = get_output(bin) init_markdown(release_notes, new_tag, release_text, bindir) title = f""SeqFu {new_tag}"" status = subprocess.run(['git', 'status', '-s'], stdout=subprocess.PIPE) if len(status.stdout.decode('utf-8')) > 0: eprint(""Uncommitted changes!"") quit(args.release) if not args.release: quit() eprint(""Preparing release"") release_cmd = ['gh', 'release', 'create', new_tag, zipfile, '--title', title, '--notes-file', changelog] try: subprocess.run(release_cmd) except Exception as e: eprint(f""Failed to release: {e}.\n# {release_cmd.join(' ')}"") try: os.rename(changelog, f""{basedir}/releases/{new_tag}.md"") except Exception as e: eprint(f""ERROR: Unable to rename {changelog}"")","Python" "Bioengineering","telatin/seqfu2","test/test-shred.sh",".sh","1788","67","#!/bin/bash export SEQFU_QUIET=1 TEMPFILENAME=$(mktemp) INPUT=""$FILES""/16S_coli.fa ### SINGLE END ""$BINDIR""/fu-shred ""$INPUT"" -l 100 -s 150 > ""$TEMPFILENAME"" COUNT=$(cat ""$TEMPFILENAME"" | ""$BINDIR""/seqfu count - | cut -f 2) LEN=$(cat ""$TEMPFILENAME"" | ""$BINDIR""/seqfu stats - | cut -f 3 | tail -n 1) EXIT=$? MSG=""SE: 10 sequences"" EXP=10 if [[ $COUNT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $COUNT from $INPUT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT from $INPUT)"" ERRORS=$((ERRORS+1)) fi MSG=""SE: Total length 1000bp "" EXP=1000 if [[ $LEN == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $LEN from $INPUT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $LEN from $INPUT)"" ERRORS=$((ERRORS+1)) fi TEMPORARY_DIR=$(mktemp -d) FWD=""$TEMPORARY_DIR""/illuminate_R1.fq REV=""$TEMPORARY_DIR""/illuminate_R2.fq ""$BINDIR""/fu-shred ""$INPUT"" -f 100 -l 50 -s 150 -o ""$TEMPORARY_DIR""/illuminate MSG=""Output found $FWD,$REV "" if [[ -e ""$FWD"" ]] && [[ -e ""$REV"" ]]; then echo -e ""$OK: $MSG "" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi COUNT=$(cat ""$FWD"" | ""$BINDIR""/seqfu count - | cut -f 2) LEN=$(cat ""$FWD"" | ""$BINDIR""/seqfu stats - | cut -f 3 | tail -n 1) MSG=""PE: 10 sequences"" EXP=10 if [[ $COUNT == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $COUNT from $INPUT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT from $INPUT)"" ERRORS=$((ERRORS+1)) fi MSG=""PE: Total length 1000bp "" EXP=500 if [[ $LEN == $EXP ]]; then echo -e ""$OK: $MSG (expected $EXP, got $LEN from $INPUT)"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG (expected $EXP, got $LEN from $INPUT)"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/hpc.sh",".sh","481","12","#!/bin/bash set -exuo pipefail VERSION=$(grep version seqfu.nimble | grep -oP \\d\+\.\\d\+\.\\d\+) make mkdir -p ""/nbi/software/testing/seqfu/${VERSION}/x86_64/bin/"" mv -v ""bin""/* ""/nbi/software/testing/seqfu/${VERSION}/x86_64/bin/"" BINSCRIPT=""/nbi/software/testing/bin/seqfu-${VERSION}"" echo '#!/bin/bash' > $BINSCRIPT echo ""VERSION=${VERSION}"" >> $BINSCRIPT echo 'export PATH=""/nbi/software/testing/seqfu/${VERSION}/x86_64/bin/:$PATH""' >> $BINSCRIPT chmod +x $BINSCRIPT ","Shell" "Bioengineering","telatin/seqfu2","test/convert.sh",".sh","506","19","FILE=$1 if [[ ! -e $FILE ]];then echo exiting.. exit 1 fi if [[ ! -d src/ ]]; then echo src should be where the script is invoked exit 1 fi set -euxo pipefail DIR=$(dirname $FILE) cp -r /Users/telatina/.choosenim/toolchains/nim-1.6.6/lib $DIR/ cp -r /Users/telatina/.nimble/pkgs $DIR/ cp -r ./src $DIR/ sed ""s'/Users/telatina/.choosenim/toolchains/nim-1.6.6/'./'g"" $FILE | sed ""s'/Users/telatina/git/seqfu2/'./'g"" > $DIR/compile.sh sed -i.bak 's|/Users/telatina/.nimble/pkgs/|./pkgs/|g' $DIR/*.c ","Shell" "Bioengineering","telatin/seqfu2","test/test-metadata.sh",".sh","1028","43","#!/bin/bash export SEQFU_QUIET=1 READS_DIR=""$FILES""/reads/ SEQFU_TEMP_DIR=$(mktemp -d) META_DEFAULT=$($BINDIR/seqfu metadata $READS_DIR > ""$SEQFU_TEMP_DIR""/metadata.tsv) META_IRIDA=$($BINDIR/seqfu metadata -f irida -P 100 $READS_DIR > ""$SEQFU_TEMP_DIR""/irida.csv) ## IUPAC EXP=3 OBS=$(""$BINDIR""/fu-tabcheck ""$SEQFU_TEMP_DIR""/metadata.tsv | cut -f 3) MSG=""Default table columns: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi EXP=6 OBS=$(""$BINDIR""/fu-tabcheck ""$SEQFU_TEMP_DIR""/metadata.tsv | cut -f 4) MSG=""Default table rows: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi EXP=7 OBS=$(getnumber $(grep . ""$SEQFU_TEMP_DIR""/irida.csv | wc -l)) MSG=""Irida lines: exp=$EXP got=$OBS"" if [[ $OBS == $EXP ]]; then echo -e ""$OK: $MSG"" PASS=$((PASS+1)) else echo -e ""$FAIL: $MSG"" ERRORS=$((ERRORS+1)) fi ","Shell" "Bioengineering","telatin/seqfu2","test/speed/hg38-fasta.md",".md","349","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `./speed/native /local/qi/db/hg38/Homo_sapiens.GRCh38.dna_sm.toplevel.fa` | 2485.163 ± 395.734 | 2050.087 | 3031.333 | 1.00 ± 0.52 | | `./speed/imported /local/qi/db/hg38/Homo_sapiens.GRCh38.dna_sm.toplevel.fa` | 2474.497 ± 1214.150 | 303.033 | 3061.138 | 1.00 | ","Markdown" "Bioengineering","telatin/seqfu2","test/speed/F09.md",".md","307","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `./speed/native /local/qi/data/SC/CEL/reads/F09.fastq.gz` | 141.438 ± 2.189 | 138.283 | 145.046 | 1.00 | | `./speed/imported /local/qi/data/SC/CEL/reads/F09.fastq.gz` | 206.206 ± 1.747 | 203.614 | 208.992 | 1.46 ± 0.03 | ","Markdown" "Bioengineering","telatin/seqfu2","test/speed/7794_51_R1.md",".md","313","5","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | |:---|---:|---:|---:|---:| | `./speed/native /local/qi/import/AN/EG/Lcr/reads/7794_51_R1.fastq` | 155.0 ± 4.7 | 149.8 | 165.8 | 1.00 | | `./speed/imported /local/qi/import/AN/EG/Lcr/reads/7794_51_R1.fastq` | 368.5 ± 17.8 | 356.0 | 412.3 | 2.38 ± 0.14 | ","Markdown" "Bioengineering","telatin/seqfu2","test/byte/validate_fastq.c",".c","5188","156","#include #include #include #define MAX_LINE_LENGTH 4096 #define QSCORE_OFFSET 33 int main(int argc, char *argv[]) { FILE *fp; int opt_offset = QSCORE_OFFSET; int opt_strict = 0; int opt_help = 0; int opt_verbose = 0; char *filename = NULL; // Initialize to NULL // Parse command-line arguments for (int i = 1; i < argc; i++) { if (strcmp(argv[i], ""-s"") == 0) { opt_strict = 1; } else if (strcmp(argv[i], ""-o"") == 0 && i < argc - 1) { opt_offset = atol(argv[i + 1]); i++; } else if (strcmp(argv[i], ""-v"") == 0) { opt_verbose = 1; } else if (strcmp(argv[i], ""-h"") == 0) { opt_help = 1; } else { filename = argv[i]; } } // Check for the correct number of command-line arguments if (opt_help) { // create a string that is the program's basename char *program_name = strrchr(argv[0], '/'); if (program_name != NULL) { program_name++; } else { program_name = argv[0]; } printf(""Usage: %s [-s] [-o offset] filename\n"", program_name); printf(""\nParameters:\n""); printf("" -s : Validate quality (optional).\n""); printf("" -o OFFSET : The offset for quality score (optional, default: 33).\n""); printf("" filename : The name of the file to be processed (optional, default: stdin)\n""); return 1; } // if defined filename open it else use stdin if ( filename != NULL ) { // print to stderr if verbose if (opt_verbose) { fprintf(stderr, ""Opening file %s\n"", filename); } fp = fopen(filename, ""r""); if (fp == NULL) { fprintf(stderr, ""Error opening file %s\n"", filename); return 1; } } else { // print to stderr if verbose if (opt_verbose) { fprintf(stderr, ""Reading from stdin\n""); } fp = stdin; } char first_seq[MAX_LINE_LENGTH]; char last_seq[MAX_LINE_LENGTH]; char line[MAX_LINE_LENGTH]; int line_count = 0; int seq_count = 0; int seq_len = 0; int valid = 1; while (fgets(line, sizeof(line), fp)) { line_count++; if (line_count % 4 == 1) { // Remove the trailing newline character line[strcspn(line, ""\n"")] = 0; // seq name: remove first character and split to the first space char *seq_name = strtok(line+1, "" ""); if (seq_count == 0) { strcpy(first_seq, seq_name); } strcpy(last_seq, seq_name); // check if first character is '@' if (line[0] != '@') { printf(""ERROR: Line %d in sequence %d does not start with '@'\n"", line_count, seq_count); valid = 0; break; } } else if (line_count % 4 == 2) { // Remove the trailing newline character line[strcspn(line, ""\n"")] = 0; seq_len = strlen(line); // Check if the line is only composed by A, C, G, T and N for (int i = 0; i < seq_len; i++) { if (line[i] != 'A' && line[i] != 'C' && line[i] != 'G' && line[i] != 'T' && line[i] != 'N') { printf(""ERROR: Line %d in sequence %d contains an invalid character: %c\n"", line_count, seq_count, line[i]); valid = 0; break; } } } else if (line_count % 4 == 3) { if (line[0] != '+') { printf(""ERROR: Line %d in sequence %d does not start with '+'\n"", line_count, seq_count); valid = 0; break; } } else if (line_count % 4 == 0) { line[strcspn(line, ""\n"")] = 0; if (seq_len != strlen(line)) { printf(""ERROR: Line %d in sequence %d has a different length than the sequence: %ld vs %d\n"", line_count, seq_count, (long)(line ? strlen(line) : 0), seq_len), seq_len); valid = 0; break; } // Check if the quality line is composed by ASCII values from 0 to 60 if (opt_strict) { int qscore_int = 0; for (int i = 0; i < seq_len; i++) { qscore_int = (int) line[i] - opt_offset; if (qscore_int < 0 || qscore_int > 60) { printf(""ERROR: Line %d in sequence %d contains an invalid quality score: %c = %d\n"", line_count, seq_count, line[i], qscore_int); valid = 0; break; } } } seq_count++; } } // create status_string char status[4]; if (valid) { strcpy(status, ""OK""); } else { strcpy(status, ""ERR""); } printf(""%s\t%d\t%s\t%s\n"", status, seq_count, first_seq, last_seq); if (fp != stdin) { fclose(fp); } return 0; } ","C" "Bioengineering","telatin/seqfu2","test/byte/shifter.c",".c","5194","149","#include #include #include #define START_BYTE_DEFAULT 128 #define BYTE_STEP_DEFAULT 64 #define MAX_BYTE_CAP_DEFAULT 256000 /* This C program allows for the manipulation of binary data within a file. It provides a versatile method to modify specific bytes within the file based on user-defined criteria. Users can choose to either increment or decrement selected bytes in the file. Usage: - To modify the file: Run the program with the desired input file as the argument. - To revert modifications: Include the '-u' option followed by the input file. The program offers flexibility by specifying the starting byte position, step size, and maximum byte cap for byte manipulation within the file. Usage: ./program_name [-u] [-s start_byte] [-j step_size] [-m max_byte] filename Options: -u : Reverts modifications made to the file (optional). -s start_byte: The starting byte position for byte manipulation (optional, default: 128). -j step_size : The step size for byte manipulation (optional, default: 64). -m max_byte : The maximum byte cap for file size (optional, default: 256000). filename : The name of the file to be processed. Andrea Telatin, QIB, 2021 */ int main(int argc, char *argv[]) { int unscramble = 0; long substitutions = 0; long start_byte = START_BYTE_DEFAULT; long byte_step = BYTE_STEP_DEFAULT; long max_byte_cap = MAX_BYTE_CAP_DEFAULT; char *filename; // Parse command-line arguments for (int i = 1; i < argc; i++) { if (strcmp(argv[i], ""-u"") == 0) { unscramble = 1; } else if (strcmp(argv[i], ""-s"") == 0 && i < argc - 1) { start_byte = atol(argv[i + 1]); i++; } else if (strcmp(argv[i], ""-j"") == 0 && i < argc - 1) { byte_step = atol(argv[i + 1]); i++; } else if (strcmp(argv[i], ""-m"") == 0 && i < argc - 1) { max_byte_cap = atol(argv[i + 1]); i++; } else { filename = argv[i]; } } // Check for the correct number of command-line arguments if (argc < 2 || filename == NULL) { // create a string that is the program's basename char *program_name = strrchr(argv[0], '/'); if (program_name != NULL) { program_name++; } else { program_name = argv[0]; } printf(""Usage: %s [-u] [-s start_byte] [-j step_size] [-m max_byte] filename\n"", program_name); printf(""\nParameters:\n""); printf("" -u : Reverts modifications made to the file (optional).\n""); printf("" -s START_BYTE : The starting byte position for byte manipulation (optional, default: 128).\n""); printf("" -j STEP_SIZE : The step size for byte manipulation (optional, default: 64).\n""); printf("" -m MAX_BYTE : The maximum byte cap for file size (optional, default: 256000).\n""); printf("" filename : The name of the file to be processed.\n""); return 1; } FILE *file = fopen(filename, ""rb+""); if (file == NULL) { fprintf(stderr, ""ERROR: Error opening file: %s\n"", filename); return 1; } // Get the file size fseek(file, 0, SEEK_END); long file_size = ftell(file); fseek(file, 0, SEEK_SET); // Cap the file_size if it exceeds max_byte_cap if (file_size > max_byte_cap) { fprintf(stderr, ""INFO:\tCapping file size to %ld bytes\n"", max_byte_cap); file_size = max_byte_cap; } // Allocate memory for reading/writing unsigned char *buffer = malloc(file_size); if (buffer == NULL) { perror(""ERROR: Memory allocation error""); fclose(file); return 1; } // Read the file into the buffer if (fread(buffer, 1, file_size, file) != file_size) { perror(""ERROR: Error reading file""); fclose(file); free(buffer); return 1; } if (unscramble) { // Unscramble the file by reverting every byte_step-th byte starting from start_byte for (long i = start_byte; i < file_size; i += byte_step) { if (buffer[i] == 0) { buffer[i] = 255; // Wrap around to the maximum value } else { buffer[i] -= 1; } substitutions++; } } else { // Scramble the file by changing every byte_step-th byte to its following, starting from start_byte for (long i = start_byte; i < file_size; i += byte_step) { if (buffer[i] == 255) { buffer[i] = 0; // Wrap around to 0 when reaching the maximum } else { buffer[i] += 1; } substitutions++; } } // Rewind the file and write the modified buffer back to it rewind(file); if (fwrite(buffer, 1, file_size, file) != file_size) { perror(""Error writing to file""); fclose(file); free(buffer); return 1; } fclose(file); free(buffer); // Print the number of substitutions printf(""INFO:\tSubstitutions: %ld\n"", substitutions); return 0; }","C" "Bioengineering","telatin/seqfu2","test/byte/validate.c",".c","7680","222","/* Description: This program reads a FASTQ file (compressed with zlib) and validates its format. It checks that the file follows the FASTQ format rules, such as having the '@' character at the beginning of the sequence identifier lines, containing only valid DNA characters, and optionally checking the quality scores for valid ASCII values. Usage: ./fastq_validator [-s] [-o offset] filename Parameters: -s : Validate quality (optional). -o OFFSET : The offset for quality score (optional, default: 33). filename : The name of the file to be processed (optional, default: stdin) */ #include #include #include #include // Include zlib header #define MAX_LINE_LENGTH 4096 #define QSCORE_OFFSET 33 int main(int argc, char *argv[]) { gzFile fp; // Use gzFile instead of FILE* int opt_offset = QSCORE_OFFSET; int opt_strict = 0; int opt_help = 0; int opt_verbose = 0; char *filename = NULL; // Initialize to NULL // Parse command-line arguments for (int i = 1; i < argc; i++) { if (strcmp(argv[i], ""-s"") == 0) { opt_strict = 1; } else if (i < argc - 1 && strcmp(argv[i], ""-o"") == 0 ) { opt_offset = atol(argv[i + 1]); i++; } else if (strcmp(argv[i], ""-v"") == 0) { opt_verbose = 1; } else if (strcmp(argv[i], ""-h"") == 0) { opt_help = 1; } else { filename = argv[i]; } } // Check for the correct number of command-line arguments if (opt_help) { // create a string that is the program's basename char *program_name = strrchr(argv[0], '/'); if (program_name != NULL) { program_name++; } else { program_name = argv[0]; } printf(""Usage: %s [-s] [-o offset] filename\n"", program_name); printf(""\nParameters:\n""); printf("" -s : Validate quality (optional).\n""); printf("" -o OFFSET : The offset for quality score (optional, default: 33).\n""); printf("" filename : The name of the file to be processed (optional, default: stdin)\n""); return 1; } // if defined filename open it else use stdin if (filename != NULL) { // print to stderr if verbose if (opt_verbose) { fprintf(stderr, ""Opening file %s\n"", filename); } fp = gzopen(filename, ""r""); // Use gzopen instead of fopen if (fp == NULL) { fprintf(stderr, ""Error opening file %s\n"", filename); return 1; } } else { // print to stderr if verbose if (opt_verbose) { fprintf(stderr, ""Reading from stdin\n""); } fp = gzdopen(fileno(stdin), ""r""); // Use gzdopen to wrap stdin } char first_seq[MAX_LINE_LENGTH]; char last_seq[MAX_LINE_LENGTH]; char line[MAX_LINE_LENGTH]; int line_count = 0; int seq_count = 0; int seq_len = 0; int valid = 1; char first_char; // read the first character if (gzread(fp, &first_char, 1) != 1) { fprintf(stderr, ""ERROR: File is empty\n""); return 1; } if (first_char == '>') { while (gzgets(fp, line, sizeof(line))) { line_count++; if (line_count == 1 || line[0] == '>') { // header seq_count++; line[strcspn(line, ""\n"")] = 0; char *seq_name = strtok(line, "" ""); if (seq_count == 1) { strcpy(first_seq, seq_name); } strcpy(last_seq, seq_name+1); } else { // sequence line[strcspn(line, ""\n"")] = 0; seq_len = strlen(line); // Check if the line is only composed by A, C, G, T and N for (int i = 0; i < seq_len; i++) { if (line[i] != 'A' && line[i] != 'C' && line[i] != 'G' && line[i] != 'T' && line[i] != 'N') { // print to stderr the error fprintf(stderr,""ERROR: Line %d in sequence %d contains an invalid character: %c\n"", line_count, seq_count, line[i]); valid = 0; break; } } } } } else if (first_char == '@') { while (gzgets(fp, line, sizeof(line))) { // Use gzgets instead of fgets line_count++; if (line_count % 4 == 1) { // Remove the trailing newline character line[strcspn(line, ""\n"")] = 0; // seq name: remove first character and split to the first space char *seq_name = strtok(line, "" ""); if (seq_count == 0) { strcpy(first_seq, seq_name); } strcpy(last_seq, seq_name+1); // check if first character is '@' if (line_count != 1 && line[0] != '@') { printf(""ERROR: Line %d in sequence %d does not start with '@'\n"", line_count, seq_count); valid = 0; break; } } else if (line_count % 4 == 2) { // Remove the trailing newline character line[strcspn(line, ""\n"")] = 0; seq_len = strlen(line); // Check if the line is only composed by A, C, G, T and N for (int i = 0; i < seq_len; i++) { if (line[i] != 'A' && line[i] != 'C' && line[i] != 'G' && line[i] != 'T' && line[i] != 'N') { // print to stderr the error fprintf(stderr,""ERROR: Line %d in sequence %d contains an invalid character: %c\n"", line_count, seq_count, line[i]); valid = 0; break; } } } else if (line_count % 4 == 3) { if (line[0] != '+') { fprintf(stderr,""ERROR: Line %d in sequence %d does not start with '+'\n"", line_count, seq_count); valid = 0; break; } } else if (line_count % 4 == 0) { line[strcspn(line, ""\n"")] = 0; if (seq_len != strlen(line)) { fprintf(stderr, ""ERROR: Line %d in sequence %d has a different length than the sequence: %ld vs %d\n"", line_count, seq_count, (long)(strlen(line) + 1), seq_len); valid = 0; break; } // Check if the quality line is composed by ASCII values from 0 to 60 if (opt_strict) { int qscore_int = 0; for (int i = 0; i < seq_len; i++) { qscore_int = (int) line[i] - opt_offset; if (qscore_int < 0 || qscore_int > 60) { fprintf(stderr,""ERROR: Line %d in sequence %d contains an invalid quality score: %c = %d\n"", line_count, seq_count, line[i], qscore_int); valid = 0; break; } } } seq_count++; } } } // create status_string char status[4]; if (valid) { strcpy(status, ""OK""); } else { strcpy(status, ""ERR""); } printf(""%s\t%d\t%s\t%s\n"", status, seq_count, first_seq, last_seq); if (fp != gzdopen(fileno(stdin), ""r"")) { // Check against gzdopen(fileno(stdin), ""r"") instead of stdin gzclose(fp); // Use gzclose instead of fclose } return 0; }","C" "Bioengineering","telatin/seqfu2","test/byte/fastx_count.c",".c","2469","88","#include #include #include #include #define BUFFER_SIZE 1024 // Function to check if the file is gzipped int is_gzipped(const char *filename) { int len = strlen(filename); return len > 3 && strcmp(filename + len - 3, "".gz"") == 0; } // Function to open the file appropriately based on its type FILE *open_file(const char *filename) { if (is_gzipped(filename)) { return (FILE *)gzopen(filename, ""rb""); } else { return fopen(filename, ""r""); } } // Function to read a line from the file char *read_line(FILE *file, char *buffer, int gzipped) { if (gzipped) { return gzgets((gzFile)file, buffer, BUFFER_SIZE); } else { return fgets(buffer, BUFFER_SIZE, file); } } // Function to check if the file is FASTQ int is_fastq(const char *filename) { return strstr(filename, "".fq"") != NULL || strstr(filename, "".fastq"") != NULL; } // Main function for parsing the FASTQ or FASTA file int main(int argc, char *argv[]) { if (argc < 2) { fprintf(stderr, ""Usage: %s \n"", argv[0]); return 1; } const char *filename = argv[1]; int gzipped = is_gzipped(filename); FILE *file = open_file(filename); if (!file) { fprintf(stderr, ""Error opening file: %s\n"", filename); return 1; } char buffer[BUFFER_SIZE]; unsigned long total_length = 0; int total_sequences = 0; int isFasta = !is_fastq(filename); int line_number = 0; while (read_line(file, buffer, gzipped) != NULL) { if (isFasta) { if (buffer[0] == '>') { // Header line in FASTA if (line_number > 0) total_sequences++; } else { total_length += strlen(buffer) - 1; // -1 to exclude the newline character } line_number++; } else { line_number++; if (line_number % 4 == 2) { // Sequence line in FASTQ total_length += strlen(buffer) - 1; // -1 to exclude the newline character total_sequences++; } } } // Adjust sequence count for the last sequence in FASTA if (isFasta && line_number > 0) total_sequences++; if (gzipped) { gzclose((gzFile)file); } else { fclose(file); } printf(""Total number of sequences: %d\n"", total_sequences); printf(""Total length of sequences: %lu\n"", total_length); return 0; }","C" "Bioengineering","telatin/seqfu2","test/byte/count.cpp",".cpp","3825","132","#include #include #include #include #include int main(int argc, char* argv[]) { std::istream* input_stream = nullptr; gzFile gz_input_stream = nullptr; std::ifstream file; bool use_gzip = false; bool use_verbose = false; bool use_stdin = true; char *input_filename = nullptr; // Check if -z flag is present for (int i = 1; i < argc; ++i) { if (strcmp(argv[i], ""-z"") == 0) { use_gzip = true; } else if (strcmp(argv[i], ""-v"") == 0) { use_verbose = true; } else { input_filename = argv[i]; use_stdin = false; // check if filename ends with .gz int len = strlen(input_filename); if (len > 3 && strcmp(input_filename + len - 3, "".gz"") == 0) { use_gzip = true; } } } // Verbose if (use_verbose) { std::cout << ""use_gzip: "" << use_gzip << std::endl; std::cout << ""use_stdin: "" << use_stdin << std::endl; std::cout << ""input_filename: "" << input_filename << std::endl; } if ( ! use_stdin ) { if (use_gzip) { gz_input_stream = gzopen(input_filename, ""rb""); if (!gz_input_stream) { std::cerr << ""Error opening gzipped file: "" << input_filename << std::endl; return 1; } } else { file.open(input_filename); if (!file) { std::cerr << ""Error opening file: "" << input_filename << std::endl; return 1; } input_stream = &file; } } else { input_stream = &std::cin; if (use_gzip) { gz_input_stream = gzdopen(0, ""rb""); // 0 is the file descriptor for stdin } } char first_char; if (use_gzip) { gzread(gz_input_stream, &first_char, 1); } else { first_char = input_stream->get(); } int greater_than_count = 0; int newline_count = 0; const int chunk_size = 1024; std::vector buffer(chunk_size); if (use_gzip) { int bytes_read; while ((bytes_read = gzread(gz_input_stream, buffer.data(), chunk_size)) > 0) { for (int i = 0; i < bytes_read; i++) { if (buffer[i] == '>') { greater_than_count++; } else if (buffer[i] == '\n') { newline_count++; } } } } else { while (input_stream->read(buffer.data(), chunk_size)) { for (int i = 0; i < chunk_size; i++) { if (buffer[i] == '>') { greater_than_count++; } else if (buffer[i] == '\n') { newline_count++; } } } // Handle the remaining characters (less than chunk_size) int remaining = input_stream->gcount(); for (int i = 0; i < remaining; i++) { if (buffer[i] == '>') { greater_than_count++; } else if (buffer[i] == '\n') { newline_count++; } } } if (file.is_open()) { file.close(); } if (gz_input_stream) { gzclose(gz_input_stream); } if (first_char == '>') { std::cout << greater_than_count + 1 << ""\tFASTA"" << std::endl; } else if (first_char == '@') { int approx = newline_count / 4; std::cout << approx << ""\tFASTQ"" << std::endl; } else { std::cerr << ""Error: first character is not '>' or '@'"" << std::endl; if (use_stdin) { std::cerr << ""If the stream is gzipped try adding -z"" << std::endl; } return 1; } return 0; } ","C++" "Bioengineering","telatin/seqfu2","test/byte/fastx_counter.c",".c","1794","71","#include #include #include #include #define BUFFER_SIZE 1024 // Function to check if the file is gzipped int is_gzipped(const char *filename) { int len = strlen(filename); return len > 3 && strcmp(filename + len - 3, "".gz"") == 0; } // Function to open the file appropriately based on its type FILE *open_file(const char *filename) { if (is_gzipped(filename)) { return (FILE *)gzopen(filename, ""rb""); } else { return fopen(filename, ""r""); } } // Function to read a line from the file char *read_line(FILE *file, char *buffer, int gzipped) { if (gzipped) { return gzgets((gzFile)file, buffer, BUFFER_SIZE); } else { return fgets(buffer, BUFFER_SIZE, file); } } // Main function for parsing the FASTQ file int main(int argc, char *argv[]) { if (argc < 2) { fprintf(stderr, ""Usage: %s \n"", argv[0]); return 1; } const char *filename = argv[1]; int gzipped = is_gzipped(filename); FILE *file = open_file(filename); if (!file) { fprintf(stderr, ""Error opening file: %s\n"", filename); return 1; } char buffer[BUFFER_SIZE]; unsigned long total_length = 0; int total_sequences = 0; int line_number = 0; while (read_line(file, buffer, gzipped) != NULL) { line_number++; if (line_number % 4 == 2) { // Sequence line total_length += strlen(buffer) - 1; // -1 to exclude the newline character total_sequences++; } } if (gzipped) { gzclose((gzFile)file); } else { fclose(file); } printf(""Total number of sequences: %d\n"", total_sequences); printf(""Total length of sequences: %lu\n"", total_length); return 0; } ","C" "Bioengineering","telatin/seqfu2","test/byte/mnt.c",".c","2326","82","#include #include #include // Required for gzipped files // Function to process a regular file void processRegularFile(FILE *file) { // Variables to keep count of sequences and total length unsigned long sequenceCount = 0; unsigned long totalLength = 0; char line[100024]; // Assuming each line will not be longer than 1024 characters while (fgets(line, sizeof(line), file)) { if (line[0] == '@') { // Sequence identifier line sequenceCount++; if (fgets(line, sizeof(line), file)) { // Sequence line totalLength += strlen(line) - 1; // -1 to remove newline character } } } printf(""Number of sequences: %lu\n"", sequenceCount); printf(""Total length: %lu\n"", totalLength); } void processGzippedFile(gzFile file) { unsigned long sequenceCount = 0; unsigned long totalLength = 0; char line[1024]; // Buffer for each line while (gzgets(file, line, sizeof(line))) { //printf(""Debug: Read line: %s"", line); // Debugging line if (line[0] == '@') { sequenceCount++; if (gzgets(file, line, sizeof(line))) { totalLength += strlen(line) - 1; // -1 to remove newline character } // discard next two lines gzgets(file, line, sizeof(line)); gzgets(file, line, sizeof(line)); } } printf(""Number of sequences: %lu\n"", sequenceCount); printf(""Total length: %lu\n"", totalLength); } int main(int argc, char *argv[]) { if (argc != 2) { fprintf(stderr, ""Usage: %s \n"", argv[0]); return 1; } FILE *file; gzFile gzfile; // Check if the file is gzipped or not if (strstr(argv[1], "".gz"")) { gzfile = gzopen(argv[1], ""r""); if (!gzfile) { fprintf(stderr, ""Could not open gzipped file: %s\n"", argv[1]); return 1; } processGzippedFile(gzfile); gzclose(gzfile); } else { file = fopen(argv[1], ""r""); if (!file) { fprintf(stderr, ""Could not open file: %s\n"", argv[1]); return 1; } processRegularFile(file); fclose(file); } return 0; } ","C" "Bioengineering","telatin/seqfu2","templates/make.sh",".sh","128","5","#!/bin/bash nim c --threads:on -d:release --opt:speed fastx_multithreaded_utility nim c -d:release --opt:speed fastx_utility_1 ","Shell" "Bioengineering","telatin/seqfu2","templates/perl/getdata.sh",".sh","241","6","#!/bin/bash set -euxo pipefail ## https://umi-tools.readthedocs.io/en/latest/Single_cell_tutorial.html#step-1-obtaining-the-data wget ""http://cf.10xgenomics.com/samples/cell-exp/1.3.0/hgmm_100/hgmm_100_fastqs.tar"" tar -x hgmm_100_fastqs.tar ","Shell" "Bioengineering","telatin/seqfu2","releases/v1.20.0.md",".md","90","3","* Added paired end support for `fu-shred` * Added `--noheader` in `seqfu stats` * Bugfixes","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.14.0.md",".md","557","8","* **SeqFu grep** will die if fed with non existing files (to ensure no wrong parameters were passed) * **SeqFu grep** will match oligos case insensitive by default * Addedd invert match `-v` to `seqfu grep` * Improved `fu-tabcheck`, notably added `--inspect` option to print columns info * `fu-split` now can use a different SeqFu than specified in path, setting `$SEQFU_BIN` or `--bin` option * `fu-split` version check fixed * :warning: Bugfix in `seqfu tab`: was not working with FASTA files * **SeqFu head** and **SeqFu tail** migrated to readfq library","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.10.0.md",".md","103","3","* Added support for MetaPhage to **seqfu metadata** * Added `--header` to **fu-tabcheck** * Minor fixes","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.8.7.md",".md","39","2","* Improved performance * Added Makefile","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.9.0.md",".md","347","5","* `seqfu grep` now has `-w` (word) and `-f` (full) match options. default behaviour unchanged. * `seqfu cat` now has a filter for Ns (`--max-ns INT`) * `seqfu cat` now has a filter for the total expected errors (`--max-ee FLOAT`), and can report `--add-ee` and `--add-initial-ee` * Added header line in `seqfu metadata` when using ""irida"" formats ","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.9.3.md",".md","203","3"," * **bugfix**: `seqfu cat` controls the length of operations (truncate, trim) * *improved*: `seqfu cat` improved renaming options (basename and strip-name will now add a progressive number automatically)","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.13.2.md",".md","179","2","* added `--print-last` option to **seqfu cat** and **seqfu heda** * updated `fu-split`, with support for paired end reads, improved performance thanks to `--print-last`, new tests","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.20.1.md",".md","117","2","* Bugfix in `seqfu metadata` when producing a **Manifest file** for **single end** * Added `--translate` to `fu-orf`","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.8.9.md",".md","21","1","* Improved **fu-msa**","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.8.8.md",".md","67","2","* Introduced the experimental multiple alignment viewer **fu-msa** ","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.12.0.md",".md","36","2","* Improved ""fu-index"" * Minor bugfix","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.9.1.md",".md","130","2","* Test suite will not fail if the version matches the remote version. Set `RELEASE=1` to enable the previous behaviour (for devs) ","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.20.3.md",".md","36","1","* Bugfix interleave/deinterleave #21","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.13.1.md",".md","33","1","* added `fu-split` (experimental)","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.9.2.md",".md","30","3","- Bugfix on Seqfu Detabulate ","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.11.0.md",".md","242","4","* Improved `seqfu stats`: added sorting option and JSON output, added GC content, improved test suite. * **bugfix** Seqfu tabulate `-d` (detabulate) was too stringent in requiring forward and reverse reads to have the same length :facepalm: ","Markdown" "Bioengineering","telatin/seqfu2","releases/v1.13.0.md",".md","221","2","* `seqfu cat` now can skip a set of initial sequences (`--skip-first INT`) or start from a specific sequence (`--jump-to`) * Minor updates in the test suite, github actions (including rich_codex) and documentation updates","Markdown" "Bioengineering","telatin/seqfu2","docs/install.md",".md","1494","46","--- layout: default title: Installation nav_order: 2 permalink: /installation --- # Installation ## Install via Miniconda The **recommended** installation method is via BioConda, which is supported from both **Linux** and **macOS**. If you have _conda_ installed ([how to install it](https://docs.conda.io/en/latest/miniconda.html)): ```bash # Ensure a recent version will be installed: 0.x is a very old and unsupported tool conda install -c conda-forge -c bioconda ""seqfu>1.10"" ``` More info on [installing conda](https://telatin.github.io/microbiome-bioinformatics/Install-Miniconda/). :warning: It is _possible_ to compile the program for Windows, but we cannot provide support for this platform at the moment. ## Pre-compiled binaries Pre-compiled core binaries are distributed with the [releases](https://github.com/telatin/seqfu2/releases), as zip files containing all the tools, labeled as ""Linux"" and ""Darwin"" as they target Linux and macOS respectively. When possible, we recommend to install SeqFu via Miniconda (see above), as it provides the full set of tools. ## Manual compilation ### Linux and macOS 1) If `nim` is not installed, install it (**[see instructions](https://nim-lang.org/install_unix.html)**). We suggest - when available - the `choosenim` method 2) Clone the repository (`git clone https://github.com/telatin/seqfu2`) 3) Compile with `nimble build`, that will download the required packages 4) The binaries will be available in the `./bin` directory ","Markdown" "Bioengineering","telatin/seqfu2","docs/intro.md",".md","4539","96","--- layout: default title: Overview nav_order: 3 permalink: /intro --- # Overview SeqFu consists of core programs, accessible as subcommands, and a set of corollary utilities, having the prefix `fu-`. Type `seqfu` alone to list the core subprograms, and `seqfu {command} --help` to access the help of each specific subcommand. To simply print the version type `seqfu version` and to print the citation `seqfu cite`. ## Basic operations: cat, head, tail, grep, rc These commands have been inspired by the common *GNU commands*, and all can read from the standard input. Their usage is quite intuitive, so here we highlight some special feature. **[seqfu cat]({{site.baseurl}}/tools/cat.html)** can read mixed FASTA and FASTQ files, and be forced to output in either FASTA or FASTQ format. Some basic manipulations are bundled, like: * Forcing FASTA or FASTQ output * Manipulating sequence name (prefix, suffix, prepend filename, remove comments...) * Add infos in the header (length, gc content, original name) * Filter by length (minimum length, maximum length, trim bases at the beginning or the end...) * ... **[seqfu grep]({{site.baseurl}}/tools/grep.html)** can be used to extract sequences by matching oligonucleotides, that would be scanned also in the reverse strand and allowing for mismatches or partial matches. The oligo can be in IUPAC alphabet with ambiguous bases (e.g. degenerate primers). **[seqfu head]({{site.baseurl}}/tools/head.html)** can skip a number of sequences (_i. e._ print the first _N_ sequences taking one every _M_), to extract a small subset sampling deeper. The _reverse complement_ function (**[seqfu rc]({{site.baseurl}}/tools/rc.html)**) is unique in taking as input both files and sequences, and properly supports IUPAC degenerate bases. ## Getting an idea: view, qual, stats, count **[seqfu view]({{site.baseurl}}/tools/view.html)** is only for interactive use, and can be used to have a visual feedback on the quality values and on the presence of oligonucleotides: ![View]({{site.baseurl}}/img/view.png) **[seqfu stats]({{site.baseurl}}/tools/stats.html)** can print the total number of sequences, bases, average, N50, N75, N90 and AuN, minimum and maximum length of a dataset, both in TSV format and with a nicer console oriented output: ```text ┌────────────────────┬───────┬──────────┬───────┬─────┬─────┬─────┬────────┬─────┬─────┐ │ File │ #Seq │ Total bp │ Avg │ N50 │ N75 │ N90 │ auN │ Min │ Max │ ├────────────────────┼───────┼──────────┼───────┼─────┼─────┼─────┼────────┼─────┼─────┤ │ filt.fa.gz │ 78730 │ 24299931 │ 308.6 │ 316 │ 316 │ 220 │ 0.385 │ 180 │ 485 │ │ illumina_1.fq.gz │ 7 │ 630 │ 90.0 │ 90 │ 90 │ 90 │ 12.857 │ 90 │ 90 │ │ illumina_2.fq.gz │ 7 │ 630 │ 90.0 │ 90 │ 90 │ 90 │ 12.857 │ 90 │ 90 │ │ illumina_nocomm.fq │ 7 │ 630 │ 90.0 │ 90 │ 90 │ 90 │ 12.857 │ 90 │ 90 │ └────────────────────┴───────┴──────────┴───────┴─────┴─────┴─────┴────────┴─────┴─────┘ ``` ## Managing datasets: interleave, deinterleave, lanes Very common tasks when dealing with Illumina Paired-End sequences are interleaving and deinterleaving the datasets. **[seqfu interleave]({{site.baseurl}}/tools/interleave.html)** and **[seqfu deinterleave]({{site.baseurl}}/tools/deinterleave.html)** can do that, with high speed and lower corruption risks. Multiple lanes can be quickly merged with **[seqfu lanes]({{site.baseurl}}/tools/merge_lanes.html)**. ## Sorting, dereplicating **[seqfu sort]({{site.baseurl}}/tools/sort.html)** can sort sequences by length. **[seqfu derep]({{site.baseurl}}/tools/derep.html)** can be used to dereplicate datasets, printing the number of identical sequences. In particular, this information can be used also from the input dataset, allowing to dereplicating a set of dereplicated files keeping trace of the number of sequences. ","Markdown" "Bioengineering","telatin/seqfu2","docs/index.md",".md","2130","44","--- layout: home title: Home nav_order: 1 --- # SeqFu [![Seqfu-Nim-Build](https://github.com/telatin/seqfu2/actions/workflows/nim-2.yaml/badge.svg)](https://github.com/telatin/seqfu2/actions/workflows/nim-2.yaml) [![pages-build-deployment](https://github.com/telatin/seqfu2/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/telatin/seqfu2/actions/workflows/pages/pages-build-deployment) [![GitHub Stars](https://img.shields.io/github/stars/telatin/seqfu2?label=⭐️)](https://github.com/telatin/seqfu2) [![Latest release](https://img.shields.io/github/v/release/telatin/seqfu2)](https://github.com/telatin/seqfu2/releases) [![Bioconda Downloads](https://img.shields.io/conda/dn/bioconda/seqfu?label=Bioconda%20Downloads)](https://anaconda.org/bioconda/seqfu) 📦 See the **[repository](https://github.com/telatin/seqfu2)** | 💾 **[releases](https://github.com/telatin/seqfu2/releases)** A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to _interleave_ and _de-interleave_ FASTQ files, to _rename_ sequences and to _count_ and print _statistics_ on sequence lengths. SeqFu is available for Linux and MacOS. * A compiled program delivering high performance analyses * Supports FASTA/FASTQ files, also Gzip compressed * A growing collection of handy utilities, also for quick inspection of the datasets * UNIX like commands but specific for sequences like `seqfu cat`, `seqfu head`, `seqfu tail`, `seqfu grep` * Terminal friendly reports from `seqfu stats` or `seqfu count`... Can be easily [installed](installation) via conda: ```bash conda install -c conda-forge -c bioconda ""seqfu>1.0"" ``` ## Citation Telatin A, Fariselli P, Birolo G. *SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files*. Bioengineering 2021, 8, 59. [doi.org/10.3390/bioengineering8050059](https://doi.org/10.3390/bioengineering8050059) ","Markdown" "Bioengineering","telatin/seqfu2","docs/usage.md",".md","2398","62","--- layout: default title: Usage Guide nav_order: 4 permalink: /usage --- # Short guide *SeqFu* is composed by a main program with multiple subprograms, and a set of utilities. Check the complete documentation for each [tool]({{site.baseurl}}/tools), that contains the detailed documentation. SeqFu has tools for: * Make life easier when working from the command line (`seqfu head`, `seqfu tail`, `seqfu rc`...) * Provide a visual feedback of datasets (like `seqfu view`) * Get statistics (`seqfu count` and `seqfu stats`) * Perform common operations with a reliable tool (`seqfu interleave`, `seqfu deinterleave`) * Perform specialistic operations with added ease of use or features ## Main program If invoked without parameters, *SeqFu* will print the list of subprograms: ```text SeqFu - Sequence Fastx Utilities version: 1.8.5 · count [cnt] : count FASTA/FASTQ reads, pair-end aware · deinterleave [dei] : deinterleave FASTQ · derep [der] : feature-rich dereplication of FASTA/FASTQ files · interleave [ilv] : interleave FASTQ pair ends · lanes [mrl] : merge Illumina lanes · list [lst] : print sequences from a list of names · metadata [met] : print a table of FASTQ reads (mapping files) · sort [srt] : sort sequences by size (uniques) · stats [st] : statistics on sequence lengths · cat : concatenate FASTA/FASTQ files · grep : select sequences with patterns · head : print first sequences · rc : reverse complement strings or files · tab : tabulate reads to TSV (and viceversa) · tail : view last sequences · view : view sequences with colored quality and oligo matches Type 'seqfu version' or 'seqfu citation' to print the version and paper, respectively. Add --help after each command to print its usage. ``` ## Subprograms *SeqFu* is bundled with an (increasing) set of utilities sharing the FASTX parsing library: * **fu-orf** to extract ORFs from Paired-End libraries * **fu-cov** to extract contigs from the most commonly used assembly programs using the coverage information printed in the headers * **fu-homocomp** to compress homopolymers (e.g. for Nanopore applications) * ... * See the **[full list](https://telatin.github.io/seqfu2/utilities/)**. ","Markdown" "Bioengineering","telatin/seqfu2","docs/notes.md",".md","3573","88","--- layout: default title: About nav_order: 8 permalink: /about --- # About SeqFu ## Citing Telatin A, Fariselli P, Birolo G. **SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files**. Bioengineering 2021, 8, 59. [https://doi.org/10.3390/bioengineering8050059](doi.org/10.3390/bioengineering8050059) ## Why There are several tools for the analysis of FASTQ/FASTA files. My personal choice has been (and is) **[SeqKit](https://bioinf.shenwei.me/seqkit/)**, a general purpose toolkit. As many other bioinformaticians, I found myself coding small _ad hoc_ scripts, for example: * A tool to extract the _index_ from Illumina FASTQ files (taking the most common occurrence from the first 1000 reads) * A tool to extract contigs using a list from a predictor * Scripts to interleave/deinterleave FASTQ files The problem was distributing a very small script to users lacking the library I was using (like the excellent [pyfastx](https://pypi.org/project/pyfastx/) or our [FASTX::Reader](https://metacpan.org/release/FASTX-Reader)). The possibility to distribute self-contained binaries was an option that was both boosting the performance of the program, and solving the dependency hell for minor applications. This led to the start of the project. ## How The main parsing library is `klib.nim` by Heng Li ([lh3/biofast](https://github.com/lh3/biofast)), that provides good performances. For some utilities the *readfq* library has been used ([andreas-wilm/nimreadfq](https://github.com/andreas-wilm/nimreadfq)). This is based on the C version of Heng Li's parsed, wrapped in an object oriented module. ## About the name The name of the program was modeled after ""[ScriptFu](https://docs.gimp.org/en/gimp-concepts-script-fu.html)"", a set of macros built in the image manipulation **GIMP**. [Apparently](https://twitter.com/StevenSalzberg1/status/1439704488508526599?s=20), in the US this might sound offensive.

I love it that these guys got away with creating a tool called 'seqfu', and even put it in the title of their paper (https://t.co/dCCUStKTEB). Did the editors/reviewers realize what this word sounds like in English? 😉 h/t @telatin https://t.co/fHvOxsKXKx

— Steven Salzberg (@StevenSalzberg1) September 19, 2021
![How to get away]({{site.baseurl}}/img/howtoget.png) So we after a consultation with Microsoft (and thanks to their previous experience with Minesweep), offer a tool to rename the program to **SeqFlower**. ![SeqFlower]({{site.baseurl}}/img/flowers.png) The renaming script is called `flower.sh` in the _src_ directory. ## Developer's details ### Perl module A Perl version of the parser is available both from **[MetaCPAN](https://metacpan.org/release/FASTX-Reader)** and from Bioconda: ``` conda install -c bioconda perl-fastx-reader ``` ### Templates The repository contains some templates to quickly write FASTX parser-based applications (in Nim or in Perl). :package: [seqfu2/templates](https://github.com/telatin/seqfu2/tree/main/templates) ## Outreach * [Slides](https://www.icloud.com/keynote/0cfGObtl14rWj_q4nZ7lFy7fg#seqfu_2) * [Slides, PDF)(http://seqfu.it/slides.pdf) ","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/tail.md",".md","1043","35","--- layout: default title: seqfu tail parent: Core Tools --- # seqfu tail *tail* is one of the core subprograms of *SeqFu*. It will print the last sequences of a FASTX file (like GNU tail), but can be instructed to skip a number of sequences between each printed one. ```text Usage: tail [options] [ ...] Options: -n, --num NUM Print the first NUM sequences [default: 10] -k, --skip SKIP Print one sequence every SKIP [default: 0] -p, --prefix STRING Rename sequences with prefix + incremental number -s, --strip-comments Remove comments -b, --basename prepend basename to sequence name --fasta Force FASTA output --fastq Force FASTQ output --sep STRING Sequence name fields separator [default: _] -q, --fastq-qual INT FASTQ default quality [default: 33] -v, --verbose Verbose output -h, --help Show this help ``` ## Screenshot ![Screenshot of ""seqfu tail""]({{site.baseurl}}/img/screenshot-tail.svg ""SeqFu tail"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/bases.md",".md","4656","83","--- layout: default title: seqfu bases parent: Core Tools --- # seqfu bases Counts the number of A, C, G, T and Ns in FASTA and FASTQ files. ```note Introduced in SeqFu 1.15.1 as experimental feature ``` Calculates the composition of DNA sequences ```text Usage: bases [options] [ ...] Print the DNA bases, and %GC content, in the input files Options: -c, --raw-counts Print counts and not ratios -t, --thousands Print thousands separator -a, --abspath Print absolute path -b, --basename Print the basename of the file -n, --nice Print terminal table -d, --digits INT Number of digits to print [default: 2] -H, --header Print header (auto enabled with --nice) -v, --verbose Verbose output --debug Debug output --help Show this help ``` ### Output The output is a table with the following columns (`-H` to print the header): 1. Filename (`-a` for absolute path, `-b` for basename) 2. Total bases (`-t` to add thousand separator) 3. Ratio of **A** bases over total bases (`-c` to print raw counts) 4. Ratio of **C** bases over total bases (`-c` to print raw counts) 5. Ratio of **G** bases over total bases (`-c` to print raw counts) 6. Ratio of **T** bases over total bases (`-c` to print raw counts) 7. Ratio of **N** bases over total bases (`-c` to print raw counts) 8. Ratio of **Other** characters (either IUPAC DNA or invalid chars) over total bases (`-c` to print raw counts) 9. %GC ratio 10. Ratio of **Uppercase** bases over total bases (if enabled by `-u`) ### Example A simple example: ```text seqfu bases --header data/illumina_* #Filename Total A C G T N Other %GC data/illumina_1.fq.gz 630 18.57 18.57 18.57 18.57 18.57 0.00 59.21 data/illumina_2.fq.gz 630 21.43 21.43 21.43 21.43 21.43 0.00 60.48 data/illumina_nocomm.fq 630 18.57 18.57 18.57 18.57 18.57 0.00 59.21 ``` when using `-n` the output is a nice table: ```text ┌─────────────────────┬───────┬────────┬────────┬────────┬────────┬──────┬───────┬────────┬───────────┐ │ File │ Bases │ A │ C │ G │ T │ N │ Other │ %GC │ Uppercase │ ├─────────────────────┼───────┼────────┼────────┼────────┼────────┼──────┼───────┼────────┼───────────┤ │ data/base_at.fa │ 33 │ 42.42 │ 0.00 │ 0.00 │ 57.58 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ │ data/bases_lower.fa │ 15 │ 33.33 │ 26.67 │ 20.00 │ 13.33 │ 6.67 │ 0.00 │ 46.67 │ 0.00 │ │ data/base_c.fa │ 5 │ 0.00 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 0.00 │ │ data/base.fa │ 2 │ 50.00 │ 50.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 50.00 │ 100.00 │ │ data/upper-none.fa │ 7 │ 42.86 │ 14.29 │ 28.57 │ 14.29 │ 0.00 │ 0.00 │ 42.86 │ 0.00 │ │ data/base_t.fa │ 5 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ │ data/base_a.fa │ 5 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ │ data/upper-lower.fa │ 10 │ 50.00 │ 50.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 50.00 │ 50.00 │ │ data/base_g.fa │ 1 │ 0.00 │ 0.00 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 100.00 │ │ data/upper-only.fa │ 9 │ 44.44 │ 11.11 │ 44.44 │ 0.00 │ 0.00 │ 0.00 │ 55.56 │ 100.00 │ │ data/base_extra.fa │ 20 │ 50.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 50.00 │ 0.00 │ 100.00 │ │ data/base_cg.fa │ 25 │ 0.00 │ 52.00 │ 48.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 100.00 │ └─────────────────────┴───────┴────────┴────────┴────────┴────────┴──────┴───────┴────────┴───────────┘ ``` ","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/interleave.md",".md","3334","81","--- layout: default title: seqfu interleave parent: Core Tools --- # seqfu interleave *interleave* (or *ilv*) is one of the core subprograms of *SeqFu*. It's used to produce an _interleaved FASTQ file_ from two separate files containing the forward and the reverse read of a paired-end fragment. ```text ilv: interleave FASTQ files Usage: ilv [options] -1 [-2 ] -f --for-tag string identifying forward files [default: auto] -r --rev-tag string identifying forward files [default: auto] -o --output save file to instead of STDOUT -c --check enable careful mode (check sequence names and numbers) -v --verbose print verbose output -s --strip-comments skip comments -p --prefix ""string"" rename sequences (append a progressive number) guessing second file: by default is scanned for _R1. and substitute with _R2. if this fails, the patterns _1. and _2. are tested. example: ilv -1 file_R1.fq > interleaved.fq ``` ## What are interleaved files? [Paired end sequences](https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html) can be stored in two separate files (usually denoted with the **_R1** and **_R2** strings) or in a single sequence where each sequence pair is stored as two subsequent sequences. A simple example is depicted below: ```text ======================================================================= File_R1.fq File_R2.fq Interleaved.fq ======================================================================= @seq1 @seq1 @seq1 TTTCATTCTGACTGCAACG GGATTAAAAAAAGAGTGTC TTTCATTCTGACTGCAACG + + + IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII @seq2 @seq2 @seq1 GTGTGGATTAAAAAAAAAA TTTTTTTTTTTTTTTTTTT GGATTAAAAAAAGAGTGTC + + + IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII @seq3 @seq3 @seq2 AGAGTGTCTGATAGCA GATAGCAG GTGTGGATTAAAAAAAAAA + + + IIIIIIIIIIIIIIII IIIIIIII IIIIIIIIIIIIIIIIIII @seq2 TTTTTTTTTTTTTTTTTTT + IIIIIIIIIIIIIIIIIII @seq3 AGAGTGTCTGATAGCA + IIIIIIIIIIIIIIII @seq3 GATAGCAG + IIIIIIII ``` ## Screenshot ![Screenshot of ""seqfu interleave""]({{site.baseurl}}/img/screenshot-interleave.svg ""SeqFu interleave"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/cat.md",".md","4048","88","--- layout: default title: seqfu cat parent: Core Tools --- # seqfu cat Concatenate multiple FASTA/FASTQ files, in a similar way of the GNU `cat` utility. ```text Usage: cat [options] [ ...] Concatenate multiple FASTA or FASTQ files. Options: -k, --skip STEP Print one sequence every STEP [default: 0] --skip-first INT Skip the first INT records [default: -1] --jump-to STR Start from the record after the one named STR (overrides --skip-first) --print-last Print the name of the last sequence to STDERR (Last:NAME) Sequence name: -p, --prefix STRING Rename sequences with prefix + incremental number -z, --strip-name Remove the original sequence name -a, --append STRING Append this string to the sequence name [default: ] --sep STRING Sequence name fields separator [default: _] -b, --basename Prepend file basename to the sequence name (before prefix) --split CHAR Split basename at this char [default: .] --part INT After splitting the basename, take this part [default: 1] --basename-sep STRING Separate basename from the rest with this [default: _] --zero-pad INT Zero pad the counter to INT digits [default: 0] Sequence comments: -s, --strip-comments Remove original sequence comments --comment-sep CHAR Comment separator [default: ] --add-len Add 'len=LENGTH' to the comments --add-initial-len Add 'original_len=LENGTH' to the comments --add-gc Add 'gc=%GC' to the comments --add-initial-gc Add 'original_gc=%GC' to the comments --add-name Add 'original_name=INITIAL_NAME' to the comments --add-ee Add 'ee=EXPECTED_ERROR' to the comments --add-initial-ee Add 'original_ee=EXPECTED_ERROR' to the comments Filtering: -n, --max-ns INT Discard sequences with more than INT Ns [default: -1] -m, --min-len INT Discard sequences shorter than INT [default: 1] -x, --max-len INT Discard sequences longer than INT, 0 to ignore [default: 0] --max-ee FLOAT Discard sequences with higher than FLOAT expected error [default: -1.0] --trim-front INT Trim INT base from the start of the sequence [default: 0] --trim-tail INT Trim INT base from the end of the sequence [default: 0] --truncate INT Keep only the first INT bases, 0 to ignore [default: 0] Negative values to print the last INT bases --max-bp INT Stop printing after INT bases [default: 0] Output: --fasta Force FASTA output --fastq Force FASTQ output --report FILE Save a report to FILE (original name, new name) --list Output a list of sequence names --anvio Output in Anvio format (-p c_ -s -z --zeropad 12 --report rename_report.txt) -q, --fastq-qual INT FASTQ default quality [default: 33] -v, --verbose Verbose output --debug Debug output -h, --help Show this help ``` ## Input One or more FASTA or FASTQ files. If no files are provided, the program will read from _standard input_. Additionally, you can add _standard input_ to the list of input files. by adding `-`. ## Output It is possible to mix FASTA and FASTQ files, and by default the program will produce a mixed output. Using `--fasta` or `--fastq` will force a specific output formats. For FASTA sequences a default quality values will be used. Using `--list` the simple list of records matching the criteria will be printed. ## Anvi'o shortcut If you use `--anvio` you will automatically suppress names and comments, and add a prefix `c_` to the sequence names and leading zeros to the counter, and write the report to `rename_report.txt`. If you specify a different `--report` file, this will of course override the default report file. ## Splashscreen ![Screenshot of ""seqfu cat""]({{site.baseurl}}/img/screenshot-cat.svg ""SeqFu cat"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/list.md",".md","1600","61","--- layout: default title: seqfu list parent: Core Tools --- # seqfu list Extract sequences from sequence files using a list of requested items. Introduced in **SeqFu 1.8**. ```text Usage: list [options] ... Print sequences that are present in a list file. Duplicated entries in the list will be ignored Other options: -c, --with-comments Include comments in the list file -p, --partial-match Allow partial matches (UNSUPPORTED) -m, --min-len INT Skip entries smaller than INT [default: 1] -v, --verbose Verbose output -r, --report Print report of found sequences --help Show this help ``` ## Input The **list** file is a simple text file with sequence names, that can contain the comments and they can have a leading `>` or `@` characters (which would be discarded). By default, if comments are present in the list they are ignored and the match is only at the sequence name level, unless the `--with-comments` option is used. ## Output The standard output is in the same format as the input files, either FASTA or FASTQ. With `--report` the full input list is printed with the total number of sequences printed. Example report: ``` # SEQUENCES REPORT # Sequence 'protein.1c;size=5372' found 1 times # Sequence 'protein.1d;size=5372' found 1 times # Sequence 'protein.missing' found 0 times # Sequence 'protein.1a;size=5372' found 1 times # Sequence 'protein.1f;size=5372' found 1 times # Sequence 'protein.notfound' found 0 times # Sequence 'protein.1b;size=5372' found 1 times Total sequences found: 5/7 ```","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/rc.md",".md","1551","66","--- layout: default title: seqfu rc parent: Core Tools --- # seqfu rc *rc* is one of the core subprograms of *SeqFu*, that allows to print the _reverse complement_ of sequences, either from input files or provided as strings. IUPAC DNA characters allowed. ```text Usage: rc [options] [...] Print the reverse complementary of sequences in files or sequences given as parameters Options: -s, --seq-name NAME Sequence name if coming as string [default: string] --strip-comments Remove sequence comments -v, --verbose Verbose output --help Show this help ``` ## Reverse complement strings To print the reverse complement of sequence, for example of universal primers with degenerate bases: ``` seqfu rc CCTACGGGNGGCWGCAG GGACTACHVGGGTATCTAATCC ``` will produce: ```text >string_1 CTGCWGCCNCCCGTAGG >string_2 GGATTAGATACCCBDGTAGTCC ``` **Note**: if a single sequence (string) is provided, the output is not in FASTA format but a plain string. This makes easier a programmatic use like: ```bash removePrimersScript.sh --for $FOR --rev $(seqfu rc $REV) ``` ## Reverse commplement files When supplying input files, the whole file will be complemented. If the file is in FASTQ format the quality will be reversed as well. The program can process multiple files. ``` seqfu rc data/test.fasta ``` will produce: ```text >SEQ1_BamHI-EcoRI ACGTGTACCAGCTACGATCGTGTGTAGCTAGCTCGTCAGCTAGCTACGTCGATCACGTACGCTGT >Seq2 with comm GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT >Seq3 GGGGGGGGGGGGGGGGGGGGG ``` ","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/trim.md",".md","1424","53","--- layout: default title: seqfu trim parent: Core Tools nav_order: 11 --- # trim The `trim` command trims FASTQ sequences from the 3' end when quality drops below a threshold in a sliding window. ## Usage ``` seqfu trim [options] [ ...] ``` ## Options | Option | Description | Default | |--------|-------------|---------| | `-w, --window-size INT` | Window size for quality calculation | 5 | | `-q, --min-avg-qual INT` | Minimum average quality within window | 20 | | `--offset INT` | Quality offset (33 for Illumina) | 33 | | `-o, --output FILE` | Output filename | stdout | | `-v, --verbose` | Verbose output | off | | `-h, --help` | Show help | | ## Description This command scans the quality scores of FASTQ sequences using a sliding window of the specified size. When the average quality within the window drops below the specified threshold, it trims the sequence from that position, discarding all subsequent bases. This is useful for removing low-quality regions from the 3' end of sequencing reads, which often contain more errors as the sequencing reaction progresses. ## Examples Trim sequences when the quality drops below 20 in a window of 5 bases: ```bash seqfu trim input.fastq -o output.fastq ``` Use a more stringent quality threshold: ```bash seqfu trim -q 25 input.fastq -o output.fastq ``` Change the window size: ```bash seqfu trim -w 10 -q 20 input.fastq -o output.fastq ```","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/count.md",".md","3039","91","--- layout: default title: seqfu count parent: Core Tools --- # seqfu count *count* (or *cnt*) is one of the core subprograms of *SeqFu*. It's used to count the sequences in FASTA/FASTQ files, and it's _paired-end_ aware so it will print the count of both files in a single line, but checking that both files have the same number of sequences. In version 1.5 the program has been redesigned to parse multiple files simultaneously. ```text Usage: count [options] [ ...] Options: -a, --abs-path Print absolute paths -b, --basename Print only filenames -u, --unpair Print separate records for paired end files -f, --for-tag R1 Forward tag [default: auto] -r, --rev-tag R2 Reverse tag [default: auto] -t, --threads INT Working threads [default: 4] -v, --verbose Verbose output -h, --help Show this help ``` ### Streaming Input from stream is supported. ### Example output Output is a TSV text with three columns: sample name, number of reads and type (""SE"" for Single End, ""Paired"" for Paired End) ```text data/test.fastq 3 SE data/comments.fastq 5 SE data/test2.fastq 3 SE data/qualities.fq 5 SE data/illumina_1.fq.gz 7 Paired ``` In case of errors will print a warning: ```text ERROR: Different counts in data/longerone_R1.fq.gz and data/longerone_R2.fq.gz # data/longerone_R1.fq.gz: 7 # data/longerone_R2.fq.gz: 2 ``` ### Multithreading Performance improvement measured on the _MiSeq SOP_ dataset from [mothur](https://mothur.org): | Command | Mean [ms] | Min [ms] | Max [ms] | Relative | |:---|---:|---:|---:|---:| | `seqfu count ../mothur-sop/*.fastq -t 4` | 142.5 ± 5.8 | 127.3 | 152.3 | 1.00 | | `seqfu count ../mothur-sop/*.fastq -t 1` | 416.5 ± 15.2 | 397.8 | 440.9 | 2.92 ± 0.16 | | `seqfu count-legacy ../mothur-sop/*.fastq` | 539.2 ± 16.6 | 519.6 | 577.4 | 3.78 ± 0.19 | ## Legacy algorithm ```text Usage: count-legacy [options] [ ...] Options: -a, --abs-path Print absolute paths -b, --basename Print only filenames -u, --unpair Print separate records for paired end files -f, --for-tag R1 Forward string, like _R1 [default: auto] -r, --rev-tag R2 Reverse string, like _R2 [default: auto] -m, --multiqc FILE Save report in MultiQC format -v, --verbose Verbose output -h, --help Show this help ``` ### MultiQC output Using the `--multiqc OUTPUTFILE` option it's possible to save a MultiQC compatible file (we recommend to use the *projectname_mqc.tsv* filename format). After coolecting all the MultiQC files in a directory, using `multiqc -f .` will generate the MultiQC report. MultiQC itself can be installed via Bioconda with `conda install -y -c bioconda multiqc`. To understand how to use MultiQC, if you never did so, check their excellent [documentation](https://multiqc.info). ### Screenshot ![Screenshot of ""seqfu count""]({{site.baseurl}}/img/screenshot-count.svg ""SeqFu cat"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/metadata.md",".md","5122","138","--- layout: default title: seqfu metadata parent: Core Tools --- # seqfu metadata Given one (or more) directories containing sequencing reads, this tool produces a metadata file by extracting the ID from the filename and optionally adding file paths or read counts. ## Usage ``` Usage: metadata [options] [...] metadata formats Prepare mapping files from directory containing FASTQ files Options: -1, --for-tag STR String found in filename of forward reads [default: _R1] -2, --rev-tag STR String found in filename of forward reads [default: _R2] -s, --split STR Separator used in filename to identify the sample ID [default: _] --pos INT... Which part of the filename is the Sample ID [default: 1] -f, --format TYPE Output format: dadaist, irida, manifest,... list to list [default: manifest] -p, --add-path Add the reads absolute path as column -c, --counts Add the number of reads as a property column (experimental) -t, --threads INT Number of simultaneously opened files (legacy: ignored) --pe Enforce paired-end reads (not supported) --ont Long reads (Oxford Nanopore) [default: false] GLOBAL OPTIONS --abs Force absolute path --basename Use basename instead of full path --force-tsv Force '\t' separator, otherwise selected by the format --force-csv Force ',' separator, otherwise selected by the format -R, --rand-meta INT Add a random metadata column with INT categories FORMAT SPECIFIC OPTIONS -P, --project INT Project ID (only for irida) --meta-split STR Separator in the SampleID to extract metadata, used in MetaPhage [default: _] --meta-part INT Which part of the SampleID to extract metadata, used in MetaPhage [default: 1] --meta-default STR Default value for metadata, used in MetaPhage [default: Cond] -v, --verbose Verbose output --debug Debug output -h, --help Show this help ``` ## Output formats SeqFu metadata now supports the following output formats: 1. **manifest**: Used as import manifest for [Qiime2](https://qiime2.org/) artifacts. 2. **qiime1**: Forward-compatible [Qiime1](http://qiime.org/) mapping file. 3. **qiime2**: [Qiime2](https://qiime2.org/) metadata file. 4. **dadaist**: [Dadaist2](https://quadram-institute-bioscience.github.io/dadaist2) compatible metadata. 5. **lotus**: [Lotus](http://lotus2.earlham.ac.uk/) mapping file (tested with Lotus1). 6. **irida**: [IRIDA uploader](https://github.com/phac-nml/irida-uploader) sample sheet. Requires `-P PROJECTID`. 7. **metaphage**: [MetaPhage](https://mattiapandolfovr.github.io/MetaPhage) metadata file. Use `--meta-split`, `--meta-part`, and `--meta-default` to customize a Treatment column. 8. **ampliseq**: [nf-core/ampliseq](https://nf-co.re/ampliseq) metadata file. 9. **rnaseq**: [nf-core/rnaseq](https://nf-co.re/rnaseq) metadata file. 10. **bactopia**: [Bactopia](https://bactopia.github.io/) FOFN (File of File Names) file. 11. **mag**: [nf-core/mag](https://nf-co.re/mag) metadata file. ## New Features - Support for `--format bactopia` to generate Bactopia FOFN files. - Added `--ont` option for long reads (Oxford Nanopore Technology). - Enhanced support for various bioinformatics pipelines (ampliseq, rnaseq, mag). ## Examples ### Manifest (default) ```bash seqfu metadata ./MiSeq_SOP/ ``` Output: ``` sample-id forward-absolute-filepath reverse-absolute-filepath F3D0 /Users/telatin/MiSeq_SOP/F3D0_S188_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D0_S188_L001_R2_001.fastq.gz F3D1 /Users/telatin/MiSeq_SOP/F3D1_S189_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D1_S189_L001_R2_001.fastq.gz ... ``` ### Qiime1 mapping file ```bash seqfu metadata MiSeq_SOP -f qiime1 --add-path --counts ``` Output: ``` #SampleID Counts Paths F3D0 7793 F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz F3D1 5869 F3D1_S189_L001_R1_001.fastq.gz,F3D1_S189_L001_R2_001.fastq.gz ... ``` ### IRIDA uploader ```bash seqfu metadata -f irida -P 123 data/pe/ ``` Output: ``` Sample_Name,Project_ID,File_Forward,File_Reverse sample1,123,sample1_R1.fq.gz,sample1_R2.fq.gz sample2,123,sample2_R1.fq.gz,sample2_R2.fq.gz ``` ### Bactopia FOFN ```bash seqfu metadata -f bactopia data/pe/ ``` For ONT data, add `--ont` Output: ``` sample runtype r1 r2 sample1 paired-end /path/to/data/pe/sample1_R1.fq.gz /path/to/data/pe/sample1_R2.fq.gz sample2 paired-end /path/to/data/pe/sample2_R1.fq.gz /path/to/data/pe/sample2_R2.fq.gz ``` ## Notes - Use `--add-path` to include full file paths in the output (when supported by the format). - The `--counts` option adds read counts to the output (experimental feature, not supported by all formats). - Format-specific options (like `--project` for IRIDA) are required for certain output types. - Use `--verbose` for detailed processing information and `--debug` for troubleshooting. For more information on each format and its specific options, please refer to the respective tool's documentation.","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/lanes.md",".md","2363","87","--- layout: default title: seqfu lanes parent: Core Tools --- # seqfu lanes ```note This function was called `merge` in a pre-release. ``` *lanes* is one of the core subprograms of *SeqFu*, that allows to quickly and easily merge Illumina lanes. ```text Usage: lanes [options] -o A program to merge Illumina lanes for a whole directory. Options: -o, --outdir DIR Output directory -e, --extension STR File extension [default: .fastq] -s, --file-separator STR Field separator in filenames [default: _] --comment-separator STR String separating sequence name and its comment [default: TAB] -v, --verbose Verbose output -h, --help Show this help ``` ## Input A directory containing files in the standard Illumina naming scheme, like: ``` ID1_S99_L001_R1_001.fastq.gz ID1_S99_L001_R2_001.fastq.gz ID1_S99_L002_R1_001.fastq.gz ID1_S99_L002_R2_001.fastq.gz ID1_S99_L003_R1_001.fastq.gz ID1_S99_L003_R2_001.fastq.gz ID1_S99_L004_R1_001.fastq.gz ID1_S99_L004_R2_001.fastq.gz ID2_S99_L001_R1_001.fastq.gz ID2_S99_L001_R2_001.fastq.gz ID2_S99_L002_R1_001.fastq.gz ID2_S99_L002_R2_001.fastq.gz ID2_S99_L003_R1_001.fastq.gz ID2_S99_L003_R2_001.fastq.gz ID2_S99_L004_R1_001.fastq.gz ID2_S99_L004_R2_001.fastq.gz ID3_S99_L001_R1_001.fastq.gz ID3_S99_L001_R2_001.fastq.gz ID3_S99_L002_R1_001.fastq.gz ID3_S99_L002_R2_001.fastq.gz ID3_S99_L003_R1_001.fastq.gz ID3_S99_L003_R2_001.fastq.gz ID3_S99_L004_R1_001.fastq.gz ID3_S99_L004_R2_001.fastq.gz ``` ## Performance If compared with an efficient Bash implementation (as described [here](https://github.com/stephenturner/mergelanes#an-easier-way)), *SeqFu* is >10X faster. | Command | Mean [ms] | Min [ms] | Max [ms] | Relative | |:---|---:|---:|---:|---:| | `seqfu merge -o /tmp/ data/lane` | 2.6 ± 0.9 | 1.6 | 10.4 | 1.00 | | `merge_lanes.sh data/lane/` | 31.8 ± 4.0 | 25.4 | 49.5 | 12.42 ± 4.46 | The _merge\_lanes.sh_ script is as follows: ```bash DIR=$PWD cd $1 ls *R1* | cut -d _ -f 1 | sort | uniq \ | while read id; do \ cat $id*R1*.fastq.gz > $id.R1.fastq.gz; cat $id*R2*.fastq.gz > $id.R2.fastq.gz; done cd $DIR/ rm $1/*.R{1,2}.* ``` and the test was performed against the `/data/lane` directory of SeqFu repository using the [hyperfine](https://github.com/sharkdp/hyperfine) program.","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/grep.md",".md","2793","92","--- layout: default title: seqfu grep parent: Core Tools --- # seqfu grep *grep* is one of the core subprograms of *SeqFu*. It can be used to select sequences by their name, comments or sequence using IUPAC degenerate oligo as query. ```text Usage: grep [options] [ ...] Print sequences selected if they match patterns or contain oligonucleotides Options: -n, --name STRING String required in the sequence name -r, --regex PATTERN Pattern to be matched in sequence name -c, --comment Also search -n and -r in the comment -f, --full The string or pattern covers the whole name (mainly used without -c) -w, --word The string or pattern is a whole word (only effective with -c, as names do not contain spaces) -i, --ignore-case Ignore case when matching names (is already enabled with regexes) -o, --oligo IUPAC Oligonucleotide required in the sequence, using ambiguous bases and reverse complement -A, --append-pos Append matching positions to the sequence comment --max-mismatches INT Maximum mismatches allowed [default: 0] --min-matches INT Minimum number of matches [default: oligo-length] -v, --verbose Verbose output --help Show this help ``` ## Get sequences by name In a sequence the name, or id, is the string before the first white space character, while we define as comment all the rest: ```text >Seq_Name_Here after the name or ID, everything else is the comment ATTACAAACAGTCGATCGTAGCTAGCTAGCTGATC ``` To extract all the sequences containing ""Here"" in the name: ``` seqfu grep -n Here file.fasta ``` If we also want to extend the search to comments we need to add the `-c` (or `--comment`) switch: ``` seqfu grep -c -n extend file.fasta ``` Finally, [regular expressions](https://www.regular-expressions.info/) are supported only enabling `-r` (or `--regex`): ``` seqfu grep -r -n Seq_N..._ file.fasta ``` ## Matching patterns in DNA sequences A simple text search (even with regular expressions) cannot be a handy way to identify matches in a DNA/RNA sequence. Using the `-o` (`--oligo`) parameter, we scan the sequence for matches of oligonucleotides supporting [IUPAC degenerate bases](https://www.bioinformatics.org/sms/iupac.html), supporting **reverse complement** matches and partial matches. ```text >Example CAGATAAAA ``` if we scan for `TTTT` we will match the sequence, as it's in the reverse complement strand: ``` seqfu -o TTTT file.fasta ``` We can also use IUPAC bases (N for any base, B for C, G or A...): ``` seqfu -o TTTTNT file.fasta ``` ## Screenshot ![Screenshot of ""seqfu grep""]({{site.baseurl}}/img/screenshot-grep.svg ""SeqFu grep"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/head.md",".md","1943","61","--- layout: default title: seqfu head parent: Core Tools --- # seqfu head *head* is one of the core subprograms of *SeqFu*. It will print the first sequences of a FASTX file (like GNU head), but can be instructed to skip a number of sequences between each printed one. ```text Usage: head [options] [ ...] Select a number of sequences from the beginning of a file, allowing to select a fraction of the reads (for example to print 100 reads, selecting one every 10). Options: -n, --num NUM Print the first NUM sequences [default: 10] -k, --skip SKIP Print one sequence every SKIP [default: 0] -p, --prefix STRING Rename sequences with prefix + incremental number -s, --strip-comments Remove comments -b, --basename prepend basename to sequence name -v, --verbose Verbose output --quiet Don't print warnings --help Show this help Output: --fasta Force FASTA output --fastq Force FASTQ output --sep STRING Sequence name fields separator [default: _] -q, --fastq-qual INT FASTQ default quality [default: 33]``` ``` ## Example By default the program prints the first 10 sequences of a file (the number can be changed with `-n` or `--num`). Sometimes to have a preview of a file we can add the `--skip` (or `-k` for short) parameter to take a sequence every _N_. The following examples shows the output of `seqfu head -n 10`, and `seqfu head -n 5 -k 4`): ![Example]({{site.baseurl}}/img/seqfu-head.png) ## Input and output `seqfu head` takes as input one ore _more_ FASTA/FASTQ files (or reads from the standard input if no filenames are provided, or `-` is added to the list). The output will be in the same format as the input, unless `--fasta` or `--fastq` are specified to force a different output. ## Screenshot ![Screenshot of ""seqfu head""](img/screenshot-head.svg ""SeqFu head"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/qual.md",".md","3627","104","--- layout: default title: seqfu qual parent: Core Tools --- # seqfu qual *qual* allows to detect the range of qualities of a FASTQ file, returning the possible encodings. Can be used to detect the last qualified position (). ```text Usage: qual [options] [...] Quickly check the quality of input files returning the detected encoding and the profile of quality scores. To read from STDIN, use - as filename. -m, --max INT Check the first INT reads [default: 5000] -l, --maxlen INT Maximum read length [default: 1000] -k, --skip INT Print one sequence every INT [default: 1] Qualified position: -w, --wnd INT Sliding window size [default: 4] -q, --wnd-qual FLOAT Minimum quality in the sliding window [default: 30.0] -z, --min-qual FLOAT Stop the sliding windows when quality is below [default: 18.0] Additional output: --gc Print GC content as extra column -p, --profile Quality profile per position (will comment the summary lines) -c, --colorbars Print graphical average quality profile Other options: -v, --verbose Verbose output -O, --offset INT Quality encoding offset [default: 33] --help Show this help ``` ## Example Check if a set of files is likely in Illumina 1.8 encoding: ``` seqfu qual data/primers/* data/primers/16S_R1.fq.gz 7.0 38.0 Sanger;Illumina-1.8; 33.42+/-8.47 249 data/primers/16S_R2.fq.gz 2.0 38.0 Sanger;Illumina-1.8; 31.96+/-9.53 205 data/primers/16Snano_R1.fq.gz 7.0 38.0 Sanger;Illumina-1.8; 33.37+/-8.63 246 data/primers/16Snano_R2.fq.gz 2.0 38.0 Sanger;Illumina-1.8; 32.05+/-9.54 220 data/primers/art_R1.fq.gz 40.0 40.0 Illumina-1.3;Sanger;Illumina-1.5;Solexa;Illumina-1.8; 40.00+/-0.00 95 data/primers/art_R2.fq.gz 40.0 40.0 Illumina-1.3;Sanger;Illumina-1.5;Solexa;Illumina-1.8; 40.00+/-0.00 93 ``` The artifical datasets (`art*`) were designed to be compatible with most encodings, while the `16S*` files are real Illumina 1.8 sequences. ## Output For each file a tab separated record is printed: 1. Filename 2. Minimum quality value 3. Maximum quality value 4. Possible encoding (semicolon separated list) 5. Mean, StDev of the quality value 6. Last qualified position 7. GC content (5 decimal positions) if enabled via `--gc` ## Per base statistics With the `--profile` option tabular overview of the quality scores per nucleotide position of the read is printed: ```text #data/primers/16Snano_R1.fq.gz 40.0 71.0 Sanger;Illumina-1.8; 66.37+/-8.63 #Pos Min Max Mean StDev Skewness 0 27.0 34.0 33.95 0.50 -12.36 1 27.0 34.0 33.97 0.46 -14.78 2 11.0 34.0 33.73 2.28 -9.08 3 23.0 34.0 33.92 0.76 -13.09 4 31.0 34.0 33.99 0.20 -15.20 5 28.0 38.0 37.76 0.86 -7.20 6 10.0 38.0 36.26 3.98 -4.89 ... 298 7.0 37.0 26.34 10.34 -0.58 299 7.0 37.0 25.62 11.23 -0.55 300 7.0 37.0 21.29 9.26 -0.09 ``` ## Graphical summary With the `--colorbar` option a graphical (Unicode) colored histogram of the _average_ quality _per base position_ is printed after each file. ![View]({{site.baseurl}}/img/qual.png) ## Use with DADA2 The last column of the tabular report (_last qualified position_), can be used to automatically detect the truncating position when using [DADA2](https://benjjneb.github.io/dada2/tutorial_1_8.html). [Dadaist](https://quadram-institute-bioscience.github.io/dadaist2/) uses *SeqFu* to automatically detect the qualified region.","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/derep.md",".md","4936","75","--- layout: default title: seqfu derep parent: Core Tools --- # seqfu derep *derep* is one of the core subprograms of *SeqFu*, that allows the dereplication of FASTA and FASTQ files. Dereplication, in R. C. Edgard [words](https://drive5.com/usearch/manual/dereplication.html) is *A rather obscure name for finding the set of unique sequences. Or, equivalently, the process of finding duplicated (replicate) sequences.* In simple words, given a FASTA file, only unique sequences will be printed in the output. A core feature is printing the number of identical sequences found in the original dataset. Dereplication is a step commonly used in NGS sequencing of amplicons, to reduce the computational time dedicated to the analysis of each representative sequence, and some tools will require dereplicated sequences as input (e.g. [USEARCH](https://rcedgar.github.io/usearch12_documentation/)). ```text Usage: derep [options] [ ...] Options: -k, --keep-name Do not rename sequence, but use the first sequence name -i, --ignore-size Do not count 'size=INT;' annotations (they will be stripped in any case) -m, --min-size=MIN_SIZE Print clusters with size equal or bigger than INT sequences [default: 0] -p, --prefix=PREFIX Sequence name prefix [default: seq] -5, --md5 Use MD5 as sequence name (overrides other parameters) -j, --json=JSON_FILE Save dereplication metadata to JSON file -s, --separator=SEPARATOR Sequence name separator [default: .] -w, --line-width=LINE_WIDTH FASTA line width (0: unlimited) [default: 0] -l, --min-length=MIN_LENGTH Discard sequences shorter than MIN_LEN [default: 0] -x, --max-length=MAX_LENGTH Discard sequences longer than MAX_LEN [default: 0] -c, --size-as-comment Print cluster size as comment, not in sequence name --add-len Add length to sequence -v, --verbose Print verbose messages -h, --help Show this help ``` ## Size values By default the program will add the number of identical sequences found to the sequence name, as USEARCH does: For example, if a sequence is found 18.335 times in the input file, the output will contain a sequence with "";size=18335"" in the name (unless `--ignore-size` is passed). The term ""size"" can be confusing, but it was adopted for compatibility with USEARCH/VSERACH. ``` >seq.1;size=18335 CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTACAGTATTCTTTTTGCCAGCGCTTAATTGCGCGGCGAAAAAACCTTACACACAGTGTTTTTTGTTATTACAAGAACTTTTGCTTTGGTCTGGACTAGAAATAGTTTGGGCCAGAGGTTTACTGAACTAAACTTCAATATTTATATTGAATTGTTATTTATTTAATTGTCAATTTGTTGATTAAATTCAAAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC >seq.2;size=4085 CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAGTTTAACTCAGAGGGTTGTAGCTGGCTCCTCCAAGAGCATGTGCACGCCCTTTGTCTTTACTCTTTTCCACCTGTGCACCTTTTGTAGACCATGAGTGAACTCTCGAGAGCGTTGGCAACGACGTGATCGGTTTGGGGATTTGCGTTCAGCTTTCCCTGTAGCTCGTGGTTTATGTCTTATAAACTCTATAGTCTGTTTTGAATGTCTTATGGGTTTTGCGCTGTAATGGTGCGACCTTTATAAACTATACAACTTTTAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC >seq.3;size=2453 CTTGGTCATTTAGAGGAAGTAAGAGAGAAATGTATAAACTCATAATTGACGAATGATAATTGTTATTGAAGTTTTTGTAAAGGGGCTTCTTTATGAATAAGGGATACACGTTTGACGATATGATTAATACCATGATGCCCCTGGCCCTTTGACGGCTCGGCAAAGGGTGAAGGAATTTACTGCACGGTCAGGCCCTCGTCGCATCGATGAAGAACGCAGC ``` To keep the size separate from the sequence name it's possible to used `-c` (`--size-as-comment`): ``` >seq.1 size=18335 CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTACAGTATTCTTTTTGCCAGCGCTTAATTGCGCGGCGAAAAAACCTTACACACAGTGTTTTTTGTTATTACAAGAACTTTTGCTTTGGTCTGGACTAGAAATAGTTTGGGCCAGAGGTTTACTGAACTAAACTTCAATATTTATATTGAATTGTTATTTATTTAATTGTCAATTTGTTGATTAAATTCAAAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC >seq.2 size=4085 CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAGTTTAACTCAGAGGGTTGTAGCTGGCTCCTCCAAGAGCATGTGCACGCCCTTTGTCTTTACTCTTTTCCACCTGTGCACCTTTTGTAGACCATGAGTGAACTCTCGAGAGCGTTGGCAACGACGTGATCGGTTTGGGGATTTGCGTTCAGCTTTCCCTGTAGCTCGTGGTTTATGTCTTATAAACTCTATAGTCTGTTTTGAATGTCTTATGGGTTTTGCGCTGTAATGGTGCGACCTTTATAAACTATACAACTTTTAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC >seq.3 size=2453 CTTGGTCATTTAGAGGAAGTAAGAGAGAAATGTATAAACTCATAATTGACGAATGATAATTGTTATTGAAGTTTTTGTAAAGGGGCTTCTTTATGAATAAGGGATACACGTTTGACGATATGATTAATACCATGATGCCCCTGGCCCTTTGACGGCTCGGCAAAGGGTGAAGGAATTTACTGCACGGTCAGGCCCTCGTCGCATCGATGAAGAACGCAGC ``` ## Summing dereplicated outputs If the input files were already dereplicated printing the ""size"" of the cluster, `derep` will sum the size values. This is a feature that to our knowledge is only available in SeqFu and allows to process in parallel multiple samples and generating a single ""dereplicated file"" at the end, propagating the correct cluster sizes. ## Screenshot ![Screenshot of ""seqfu derep""]({{site.baseurl}}/img/screenshot-derep.svg ""SeqFu derep"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/merge.md",".md","1828","57","--- layout: default title: seqfu merge parent: Core Tools --- # seqfu merge ```note Function under development: APIs and default parameters are likely going to change. This is why you don't see it listed in the main screen of SeqFu (yet). ``` A tool to naively merge paired end reads preserving the quality of the forward read. ``` Usage: merge [options] -1 File_R1 Options: -1, --R1 FILE First paired-end file -2, --R2 FILE Second paired-end file, can be automatically inferred -i, --minid FLOAT Minimum identity [default: 0.80] -m, --minlen INT Minimum overlap [default: 20] --accepted-identity FLOAT Accept fusion when identity is above FLOAT [default: 0.96] -v, --verbose Print verbose messages -h, --help Show this help ``` ## Merging reads There are several tools to merge overlapping reads, and some are better than others. In particular if we use tools that correcly interpret the _Phred quality scores_, then tools like USEARCH and VSEARCH are correcly recalibrating the quality of the overlapping bases. Some tools, however, are expeting quality scores that are more likely produced by a sequencing tool. This experimental module of SeqFu joins the reads in a different way: takes the forward read _as is_, and extends it with the (reverse complemented) missing part taken from the R2. ## Potential uses This tool can be used to estimate the overlapping size or the ""mergeability"" of reads before using the tools of choice. For example: ``` seqfu merge -1 reads_R1.fq | seqfu head -n 200 | seqfu stats -n ``` ## Output The merged reads are printed to the standard output. Also this is somehow unusual compared with most mergin tools, but allows streaming which is a core feature in SeqFu tools.","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/tabulate.md",".md","2849","99","--- layout: default title: seqfu tabulate parent: Core Tools --- # seqfu tabulate ```note This tool has been introduced with seqfu 1.2.2 ``` This program converts a sequence file (FASTA or FASTQ) to a tabular file, and vice versa. Several Unix tools can process a stream of information line-by-line, and tabular file can be easily modified and filtered piping serveral programs. This tool will allow to **tabulate** (convert to TSV) and **detabulate** (convert to FASTX) sequences. ``` Usage: tabulate [options] [] Convert FASTQ to TSV and viceversa. Single end is a 4 columns table (name, comment, seq, qual), paired end have 4 columns for the R1 and 4 columns for the R2. Paired end reads need to be supplied as interleaved. Options: -i, --interleaved Input is interleaved (paired-end) -d, --detabulate Convert TSV to FASTQ (if reading from file is autodetected) -c, --comment-sep CHAR Separator between name and comment (default: tab) -s, --field-sep CHAR Field separator (default: tab) -v, --verbose Verbose output -h, --help Show this help ``` ## Tabular format The conversion works as follows: * FASTA files are converted to a 3 columns table: name, comments and sequence * Single-End FASTQ files are converted to a 4 columns table: name, comments, sequence and quality * Paired-End FASTQ (interleaved) files are converted to 8 colums table: R1 name, comments, sequence and quality and R2 name, comments, sequence and quality To allow an efficient use of streams, paired-end datasets need to be interleaved (see: _seqfu interleave_). To make an example this FASTQ file: ``` @read_1 tag=A ATTACAATTACAATTACAA + EAFFFFFABBBAAAAAAAC @read_2 tag=B GGACAGAATTACAATTTTT + FFFFFFFFABBBAAAAAAA ``` will become: ``` read_1 tag=A ATTACAATTACAATTACAA EAFFFFFABBBAAAAAAAC read_2 tag=B GGACAGAATTACAATTTTT FFFFFFFFABBBAAAAAAA ``` ## Conversions ### Sequence to table A single file can be converted to tabular format. *NOTE*: If the file is automatically detected as interleaved (the first and second read have the same name) you can omit `-i` (or `--interleave`), but we recommend to use it to make the command clearer. ``` seqfu tabulate file.fastq | gzip -c > tabular.tab.gz ``` ### Table to sequences When a file is provided, the input format is automatically detected. Otherwise specify `-d` (or `--detabulate` to convert from table to FASTX). ``` seqfu tabulate file.tab > sequences.fq ``` or, via _stream_: ``` cat file.tab.gz | seqfu tabulate --detabulate > sequences.fq ``` ### Pipeline We designed the tool to provide a simple way to make ad hoc modifications via tabular lines, so a full workflow could be: ``` seqfu interleave ... | seqfu tabulate | CUSTOM_STEP | seqfu tabulate --detabulate | seqfu deinterleave -o basename - ``` ","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/check.md",".md","5231","139","--- layout: default title: seqfu check parent: Core Tools --- # seqfu check ```note **EXPERIMENTAL**: Introduced in SeqFu 1.15, updated with --deep in 1.18 (see below). In SeqFu 2.0 a strict behaviour will be used by default, see **fu-pecheck** and **fu-secheck**. ``` Evaluates the integrity of DNA FASTQ files. ```text Usage: seqfu check [options] [] seqfu check [options] --dir Check the integrity of FASTQ files, returns non zero if an error occurs. Will print a table with a report. Input is a single dataset: the forward read file the reverse read file or a directory of FASTQ files (--dir): the directory containing the FASTQ files Options: -d, --deep Perform a deep check of the file and will not lsupport multiline Sanger FASTQ [default: false] -n, --no-paired Disable autodetection of second pair -s, --safe-exit Exit with 0 even if errors are found -q, --quiet Do not print infos, just exit status -v, --verbose Verbose output -t, --thousands Print numbers with thousands separator --debug Debug output -h, --help Show this help ``` ### Integrity check :warning: If not using `--deep`, the file is considered valid if `seqfu cat $INPUT > $OUTPUT` would produce a valid file (i.e. if an error is detected at the 100-th sequence, the file would be considered valid reporting 99 as total sequences) A single FASTQ file is considered valid if: * each record has the same sequence and quality length * only A,C,G,T,N characters are present in the sequence A paired-end set of FASTQ files is considered valid if: * each file is individually valid * the two files have the same number of sequences * the first and last sequence of both files has the same name (the last three characters are ignored if the remaining sequence name is greater than 4 characters) * the first and last sequence of the two files are not identical (R1 != R2) ### Deep check If you are parsing NGS files, i.e. FASTQ files, with four lines per record and you expect them to be accepted by any program, use `--deep`. ### Usage To test a single file: ```bash seqfu check test_file.fq.gz ``` To test a pair of files: ```bash seqfu check test_R1.fq.gz [test_R2.fq.gz] ``` Note that if supplying a single file but a matching pair is detected (e.g. `test_R1.fq.gz` is supplied and `test_R2.fq.gz` is found), the check will be performed on both files. To test all files in a directory: ```bash seqfu check --dir test_dir ``` #### Other options * `--no-paired` disables the autodetection of the second pair (i.e. force single end check) * `--thousands` will add a thousands separator to the output * `--quiet` will not print data, but only the exit status will be used * `--verbose` will print more information (including processing speed) * `--debug` will print debug information * `--safe-exit` will always exit with 0, even if errors are found (useful in pipelines) ### Exit status If an error is identified in at least one file, the program will exit with non zero status, unless the `--safe-exit` option is used. ### Output The output is a table with the following columns: 1. Status (`OK` or `ERR`) 2. Library type (`SE` or `PE`) 3. Filename (the path to the first pair, if `PE`) 4. Number of sequences counted (if `PE`: number of sequences in **both** files) or `-` if the dataset is not valid 5. Number of bases (if `PE`: total number of bases in **both** files) or `-` if the dataset is not valid 6. Number of errors 7. List of detected errors (if any) #### Example Example of output for a directory containing 3 Paired End datasets: ```text OK PE /tmp/data/16S_R1.fq.gz 12274 3694474 0 OK PE /tmp/data/16Snano_R1.fq.gz 468 140868 0 OK PE /tmp/data/illumina_1.fq.gz 14 1260 0 ``` Example of errors (can be reproduced using the *data* directory of the repository) ```bash seqfu check --dir data/primers ``` ```text OK SE data/primers/16S_merge.fq.gz 6137 2596981 0 OK SE data/primers/16S_vsearch_merge.fq.gz 3935 1818111 0 ERR SE data/primers/artificial.fq.gz - - 2 Invalid character in sequence: < > in R2.REV+.middle; OK SE data/primers/its-merge.fq.gz 7299 1504898 0 OK SE data/primers/se.fq.gz 234 70434 0 OK SE data/primers/small.fq 4 360 0 OK PE data/primers/16S_R1.fq.gz 12274 3694474 0 OK PE data/primers/16Snano_R1.fq.gz 468 140868 0 ERR PE data/primers/art_R1.fq.gz 7 - 5 R2=Invalid character in sequence: < > in R2.REV+.middle;;First sequence names do not match (R1.startFOR+, R2.startREV+);Last sequence names do not match (R1.FOR1+.start-middle, ); OK PE data/primers/its_R1.fq.gz 16000 3387804 0 OK PE data/primers/itsfilt_R1.fq.gz 15618 3272396 0 OK PE data/primers/pico_R1.fq.gz 24 7224 0 ```","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/tofasta.md",".md","4466","144","# seqfu tofasta Converts various sequence file formats to FASTA format. ```note Introduced in SeqFu 1.23.0 ``` A versatile format converter supporting multiple bioinformatics file formats including sequence alignments, genome annotations, and assembly graphs. The tool automatically detects the input format and converts sequences to standard FASTA format. Replicates the approach of [any2fasta](https://github.com/tseeman/any2fasta), but it's faster. ```text Usage: tofasta [options] ... Convert various sequence formats to FASTA format. Options: -n, --replace-iupac Replace non-IUPAC characters with 'N' -l, --to-lowercase Convert sequences to lowercase -u, --to-uppercase Convert sequences to uppercase -o, --output FILE Write output to FILE (default: stdout) Note: checks for duplicate IDs across all files -v, --verbose Print progress information to stderr -h, --help Show this help ``` ## Supported Formats `seqfu tofasta` automatically detects and converts the following formats: | Format | Description | Notes | |--------|-------------|-------| | FASTA | Standard FASTA format | Pass-through with optional transformations | | FASTQ | Sanger, Illumina, Solexa | Quality scores are discarded | | GenBank | NCBI GenBank flat file | Extracts sequences from ORIGIN section | | EMBL | EMBL-Bank format | Extracts sequences from SQ section | | GFF | Generic Feature Format | Extracts sequences after `##FASTA` directive | | GFA | Graphical Fragment Assembly | Extracts sequences from S (segment) lines | | Clustal | Clustal W alignment | Preserves gaps in sequences | | Stockholm | Stockholm alignment | Converts '.' gaps to '-' | ## Options **`-n, --replace-iupac`** Replaces non-standard IUPAC characters with 'N'. Standard IUPAC codes (A, T, G, C, N) are preserved, while ambiguous codes (R, Y, W, S, K, M, etc.) are replaced with 'N'. **`-l, --to-lowercase`** Converts all sequence characters to lowercase. Useful for soft-masking or compatibility with tools that expect lowercase input. **`-u, --to-uppercase`** Converts all sequence characters to uppercase. Takes precedence over `-l` if both are specified. **`-o, --output FILE`** Writes all sequences to a single output file instead of stdout. When using this option, the tool performs duplicate ID checking across all input files and will exit with an error if duplicate sequence IDs are found. **`-v, --verbose`** Prints progress information to stder ## Examples ### Basic Format Conversion Convert a GenBank file to FASTA: ```bash seqfu tofasta genome.gbk > genome.fasta ``` Convert a FASTQ file (quality scores are discarded): ```bash seqfu tofasta reads.fastq.gz > reads.fasta ``` ### Multiple Files Process multiple files and combine into one FASTA file: ```bash seqfu tofasta -o combined.fasta file1.gbk file2.gff file3.fastq.gz ``` Replace ambiguous IUPAC codes with N: ```bash seqfu tofasta -n -u sequences.fasta > clean.fasta ``` ### Input Handling - **Gzip Support**: All input files can be gzip-compressed (`.gz` extension) - **No STDIN**: Currently, `tofasta` requires file arguments and does not support reading from standard input - **Format Detection**: File format is automatically detected from content, not file extension - **Error Handling**: The tool is strict and will exit with an error on unknown or malformed formats ### Duplicate ID Detection When using `-o/--output`, the tool checks for duplicate sequence IDs across all input files: ```bash # This will fail if seq1.gbk and seq2.gbk contain sequences with the same ID seqfu tofasta -o combined.fasta seq1.gbk seq2.gbk ``` Error message example: ``` ERROR: Duplicate sequence ID found: NZ_12345 First occurrence in a previous file Second occurrence in: seq2.gbk ``` ### Format-Specific Behavior **GenBank/EMBL**: - Extracts accession number as sequence ID - Extracts sequence from ORIGIN/SQ section - Handles multiple records in a single file **GFF**: - Only processes sequences after `##FASTA` directive - Ignores feature annotations - Preserves sequence IDs from FASTA headers **Clustal/Stockholm**: - Preserves alignment gaps in output - Concatenates sequence fragments if alignment spans multiple blocks - Stockholm '.' gaps are converted to '-' **GFA**: - Only processes S (segment) lines - Uses segment name as sequence ID - Ignores paths, links, and other graph elements ","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/stats.md",".md","6692","161","--- layout: default title: seqfu stats parent: Core Tools --- # seqfu stats *stats* is one of the core subprograms of *SeqFu*. ```note Version prior to v1.22.1 were calculatin auN incorrectly ``` ```text Usage: stats [options] [ ...] Options: -a, --abs-path Print absolute paths -b, --basename Print only filenames -n, --nice Print nice terminal table -j, --json Print json (EXPERIMENTAL) -s, --sort-by KEY Sort by KEY from: filename, counts, n50, tot, avg, min, max descending for values, ascending for filenames [default: none] -r, --reverse Reverse sort order -t, --thousands Add thousands separator (only tabbed/nice output) --csv Separate output by commas instead of tabs --gc Also print %GC --multiqc FILE Saves a MultiQC report to FILE (suggested: name_mqc.txt) --precision INT Number of decimal places to round to [default: 2] --noheader Do not print header -v, --verbose Verbose output -h, --help Show this help ``` ### Sorting ```note Sorting added in SeqFu 1.11. ``` To sort by filename (ascending alphabetical order) add `--sort filename`. Numerical values are sorted from the largest (descending), supported values are: * *n50*, *n75* or *N90* * *count* or *counts* (number of reads) * *sum* or *tot* (total bases) * *min* or *minimum* (minimum length) * *max* or *maximum* (maximum length) * *avg* or *mean* (average length) * *aun* (area under the Nx curve) **NOTE** Specifying an invalid key will result in unsorted results with a warning, but in future releases this might throw an error. ### Example output Output is a TSV text with three columns (or CSV using `--csv`): ```text File,#Seq,Sum,Avg,N50,N75,N90,Min,Max data/filt.fa.gz,78730,24299931,308.6,316,316,220,180,485 ``` ### Screen friendly output When using `-n` (`--nice`) output: ```text seqfu stats data/filt.fa.gz -n ┌─────────────────┬───────┬──────────┬───────┬─────┬─────┬─────┬───────┬─────┬─────┐ │ File │ #Seq │ Total bp │ Avg │ N50 │ N75 │ N90 │ auN │ Min │ Max │ ├─────────────────┼───────┼──────────┼───────┼─────┼─────┼─────┼───────┼─────┼─────┤ │ data/filt.fa.gz │ 78730 │ 24299931 │ 308.6 │ 316 │ 316 │ 220 │ 0.385 │ 180 │ 485 │ └─────────────────┴───────┴──────────┴───────┴─────┴─────┴─────┴───────┴─────┴─────┘ ``` ## MultiQC output Using the `--multiqc OUTPUTFILE` option it's possible to save a MultiQC compatible file (we recommend to use the *projectname_mqc.tsv* filename format). After coolecting all the MultiQC files in a directory, using `multiqc -f .` will generate the MultiQC report. MultiQC itself can be installed via Bioconda with `conda install -y -c bioconda multiqc`. To understand how to use MultiQC, if you never did so, check their excellent [documentation](https://multiqc.info). ## Legacy The pre 1.11 version of the statistics has been made available via `seqfu oldstats`. There are no breaking changes at the moment, and an expanded set of tests ensures the compatibility not only of the metrics (unchanged) but also of the output (now supporting sorting options). ## Benchmark A similar functionality is provided by `SeqKit`, so we compared the performance of SeqFu with [SeqKit](https://bioinf.shenwei.me/seqkit/) and [n50](https://metacpan.org/pod/release/PROCH/Proch-N50-1.3.0/bin/n50), both available from bioconda. We used a Linux Virtual Machine running Ubuntu 18.04, with 8 cores and 64 Gb of RAM for the test, with Miniconda (4.9.2) to install the required tools. :warning: SeqKit, by default, omits N50 calculation, that is a core feature (always enabled) in SeqFu. The correct comparison is thus between `seqfu stats` and `seqkit stats --all`. Speed evaluate with [hyperfine](https://github.com/sharkdp/hyperfine), peak memory usage with this [bash script](https://gist.github.com/MattForshaw/86b82b6c09bdbfce5ff5ee570e8a8bef). As dataset we used the Human Genome (see [this benchmark page](https://bioinf.shenwei.me/seqkit/benchmark/)), which contains few large sequences, and the reference genome of the gastrointestinal tract, which is composed by many short sequences instead. The test can be replicated with these commands: ```bash # Download tools (can be done in a new environment) conda install -c conda-forge -c bioconda hyperfine n50=1.3.0 seqkit=0.16.0 seqfu=0.9.6 # Download datasets: many short sequences and few large sequences wget http://downloads.hmpdacc.org/data/reference_genomes/body_sites/Gastrointestinal_tract.nuc.fsa wget ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz # Compare execution times FILE1=Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz FILE2=Gastrointestinal_tract.nuc.fsa for FILE in $FILE1 $FILE2; do hyperfine --export-markdown stat_$(basename $FILE | cut -f1 -d.).md --warmup 1 --min-runs 3 \ ""seqfu stats $FILE"" \ ""seqkit stats $FILE"" \ ""seqkit stats --all $FILE"" \ ""n50 -x $FILE"" done ``` The result, for the **Human Genome** (few large sequences), has been: | Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `seqfu stats $FILE` | 27.420 ± 0.349 | 27.090 | 27.785 | 1.00 | | `seqkit stats $FILE` :warning: | 116.693 ± 0.236 | 116.512 | 116.960 | 4.26 ± 0.05 | | `seqkit stats --all $FILE` | 120.435 ± 0.434 | 120.054 | 120.907 | 4.39 ± 0.06 | | `n50 -x $FILE` | 34.888 ± 0.628 | 34.167 | 35.316 | 1.27 ± 0.03 | For the **Gastrointestinal reference genomes** (many short sequences): | Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `seqfu stats $FILE` | 6.885 ± 0.307 | 6.602 | 7.211 | 1.82 ± 0.09 | | `seqkit stats $FILE` :warning: | 3.793 ± 0.082 | 3.699 | 3.854 | 1.00 | | `seqkit stats --all $FILE` | 7.667 ± 0.081 | 7.583 | 7.746 | 2.02 ± 0.05 | | `n50 -x $FILE` | 76.377 ± 1.990 | 74.891 | 78.638 | 20.14 ± 0.68 | ## Screenshot ![Screenshot of ""seqfu stats""]({{site.baseurl}}/img/screenshot-stats.svg ""SeqFu stats"") ","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/view.md",".md","3116","92","--- layout: default title: seqfu view parent: Core Tools --- # seqfu view *view* is one of the core subprograms of *SeqFu*. It can be used to visually inspect a FASTQ file printing colored bars for quality scores and highlighting oligonucleotide matches. ```text Usage: view [options] [] View a FASTA/FASTQ file for manual inspection, allowing to search for an oligonucleotide. Options: -o, --oligo1 OLIGO Match oligo, with ambiguous IUPAC chars allowed (rev. compl. search is performed), color blue -r, --oligo2 OLIGO Second oligo to be scanned for, color red -q, --qual-scale STR Quality thresholds, seven values separated by columns [default: 3:15:25:28:30:35:40] --match-ths FLOAT Oligo matching threshold [default: 0.75] --min-matches INT Oligo minimum matches [default: 5] --max-mismatches INT Oligo maxmimum mismataches [default: 2] --ascii Use simple ASCII chars instead of UNICODE to render the quality values -Q, --qual-chars Show quality characters instead of bars -n, --nocolor Disable colored output --verbose Show extra information -h, --help Show this help ``` ## Example output The quality scores are rendered as colored bars (grey, red, yellow, green) of different heights. Matching oligos are rendered as blue arrows (forward) or red arrows (reverse). ![Screenshot of ""seqfu view, action""]({{site.baseurl}}/img/screenshot-view-example.svg ""SeqFu view example"") ## Important hints ### Disabling wordwrap _SeqFu view_ is designed for a manual inspection, and thus it's very convenient to pipe the output to `less` to avoid being misled by word-wraps: ```bash seqfu view sequence.fq | less -SR ``` (in `less`: `-S` prevents word-wrap, and `-R` will preserve the colored output) ### Encoding of ""graphical"" bars The _graphical_ rendering of the quality values is done using Unicode characters (UTF-8 encoding), thus requiring both the host system and the terminal emulator to support UTF-8. A simple test to check if your terminal supports Unicode is to type: ```bash echo -e '\xe2\x82\xac' ``` If you see the Euro character (€) then your terminal fully supports UTF-8. If not, you can use `--ascii` or `--qual-chars`. The following screenshot shows how quality scores are rendered using the different options: * Default view with quality scale ![Screenshot: Quality scale""]({{site.baseurl}}/img/screenshot-view-qual.svg ""SeqFu view: quality scale"") * Graphical representation of the quality with ASCII characters ![Screenshot: Quality scale in ASCII]({{site.baseurl}}/img/screenshot-view-qual-ascii.svg ""Qualities in ASCII chars"") * Quality encoded as in the FASTQ file, but colored ![Screenshot: Quality scale as in FASTQ]({{site.baseurl}}/img/screenshot-view-qual-raw.svg ""Qualities as encoded in FASTQ"") ## Screenshot ![Screenshot of ""seqfu view, help""]({{site.baseurl}}/img/screenshot-view.svg ""SeqFu view"") ","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/deinterleave.md",".md","3401","88","--- layout: default title: seqfu deinterleave parent: Core Tools --- # seqfu deinterleave *deinterleave* (or *dei*) is one of the core subprograms of *SeqFu*. It's used to produce two separate FASTQ files from an interleaved file. ```text ilv: interleave FASTQ files Usage: dei [options] -o basename -o --output-basename ""str"" save output to output_R1.fq and output_R2.fq -f --for-ext ""R1"" extension for R1 file [default: _R1.fq] -r --rev-ext ""R2"" extension for R2 file [default: _R2.fq] -c --check enable careful mode (check sequence names and numbers) -v --verbose print verbose output -s --strip-comments skip comments -p --prefix ""string"" rename sequences (append a progressive number) notes: use ""-"" as input filename to read from STDIN example: dei -o newfile file.fq ``` ### Streaming If a program produce an interleaved output, `seqfu deinterleave` can be used in a pipe (specifying ""-"" as input): ```bash fu-primers -1 file_R1.fq -2 file_R2.fq | seqfu deinterleave -o fileNoPrimers - ``` ## What are interleaved files? [Paired end sequences](https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html) can be stored in two separate files (usually denoted with the **_R1** and **_R2** strings) or in a single sequence where each sequence pair is stored as two subsequent sequences. A simple example is depicted below: ```text ======================================================================= File_R1.fq File_R2.fq Interleaved.fq ======================================================================= @seq1 @seq1 @seq1 TTTCATTCTGACTGCAACG GGATTAAAAAAAGAGTGTC TTTCATTCTGACTGCAACG + + + IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII @seq2 @seq2 @seq1 GTGTGGATTAAAAAAAAAA TTTTTTTTTTTTTTTTTTT GGATTAAAAAAAGAGTGTC + + + IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII @seq3 @seq3 @seq2 AGAGTGTCTGATAGCA GATAGCAG GTGTGGATTAAAAAAAAAA + + + IIIIIIIIIIIIIIII IIIIIIII IIIIIIIIIIIIIIIIIII @seq2 TTTTTTTTTTTTTTTTTTT + IIIIIIIIIIIIIIIIIII @seq3 AGAGTGTCTGATAGCA + IIIIIIIIIIIIIIII @seq3 GATAGCAG + IIIIIIII ``` ## Screenshot ![Screenshot of ""seqfu deinterleave""]({{site.baseurl}}/img/screenshot-deinterleave.svg ""SeqFu deinterleave"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/sort.md",".md","618","28","--- layout: default title: seqfu sort parent: Core Tools --- # seqfu sort *sort* is one of the core subprograms of *SeqFu*, that allows sorting a FASTA/FASTQ file by sequence size. ```text Usage: sort [options] [ ...] Sort sequences by size printing only unique sequences Options: -p, --prefix STRING Sequence prefix -s, --strip-comments Remove sequence comments --asc Ascending order -v, --verbose Verbose output -h, --help Show this help ``` ## Screenshot ![Screenshot of ""seqfu sort""]({{site.baseurl}}/img/screenshot-sort.svg ""SeqFu sort"")","Markdown" "Bioengineering","telatin/seqfu2","docs/tools/rotate.md",".md","1767","92","--- layout: default title: seqfu rotate parent: Core Tools --- # seqfu rotate Rotate a sequence setting a new starting position, using a new position or an oligonucleotide. Introduced with SeqFu 1.8.6. ```text sage: fu-rotate [options] -i POS [...] fu-rotate [options] -m STR [...] Rotate the sequences of one or more sequence files using coordinates or motifs. Position based: -i, --start-pos POS Restart from base POS, where 1 is the first base [default: 1] Motif based: -m, --motif STR Rotate sequences using motif STR as the new start, where STR is a string of bases -s, --skip-unmached If a motif is provided, skip sequences that do not match the motif -r, --revcomp Also scan for reverse complemented motif Other options: -v, --verbose Verbose output -h, --help Show this help ``` ## Examples Given an input file with a single sequence: ```text >polyA ACACGTACTACTGAAAAAAAAAACTGCTACTA ``` ### Rotate by new position ```bash seqfu rotate -i 14 data/homopolymer.fa ``` Output: ```text >polyA AAAAAAAAAACTGCTACTAACACGTACTACTG ``` ### Rotate by oligonucleotide :warning: rotation by oligo will only produce an output if the match is unique ```bash seqfu rotate -m AAAAAAAAAA data/homopolymer.fa ``` Output: ```text >polyA AAAAAAAAAACTGCTACTAACACGTACTACTG ``` ### Rotate by oligonucleotide (also in reverse) ```bash seqfu rotate -r -m GTTTTTTTTTT data/homopolymer.fa ``` Output: ```text >polyA GTTTTTTTTTTCAGTAGTACGTGTTAGTAGCA ``` ## Screenshot ![Screenshot of ""seqfu rotate""]({{site.baseurl}}/img/screenshot-rotate.svg ""SeqFu rotate"")","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-primers.md",".md","1367","34","--- layout: default title: fu-primers parent: Utilities --- # fu-primers A program to remove primers from the raw output (FASTQ) of amplicons, allowing IUPAC degenerate bases and checking for multiple occurrences (dimers/concatamers). ```text Usage: fu-primers [options] -1 [-2 ] This program currently only supports paired-end Illumina reads. Options: -1 --first-pair First sequence in pair -2 --second-pair Second sequence in pair (can be guessed) -f --primer-for FOR Sequence of the forward primer [default: CCTACGGGNGGCWGCAG] -r --primer-rev REV Sequence of the reverse primer [default: GGACTACHVGGGTATCTAATCC] -m --min-len INT Minimum sequence length after trimming [default: 50] --primer-thrs FLOAT Minimum amount of matches over total length [default: 0.8] --primer-mismatches INT Maximum number of missmatches allowed [default: 2] --primer-min-matches INT Minimum numer of matches required [default: 8] --primer-pos-margin INT Number of bases from the extremity of the sequence allowed [default: 2] --pattern-R1 Tag in first pairs filenames [default: auto] --pattern-R2 Tag in second pairs filenames [default: auto] -v --verbose Verbose output -h --help Show this help ``` ","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-shred.md",".md","4492","112","--- layout: default title: fu-shred parent: Utilities --- # fu-shred ```note Since 1.18 paired end support was enabled ``` A program to systematically shotgun a reference (i.e. this does **not** simulate a random shotgun library preparation, but produce reads of length _L_ sliding over the reference chromosomes at a step _S_). This tool is to test the effect of read size alone on alignment and classification methods, and was introduced in SeqFu 1.4. ```text Usage: fu-shred [options] [...] Systematically produce a ""shotgun"" of input sequences. Can read from standard input. Options: -l, --length INT Segment length [default: 100] -s, --step INT Distance from one segment start to the following [default: 10] -q, --quality INT Quality (constant) for the segment, if -1 is provided will be printed in FASTA [default: 40] -r, --add-rc Print every other read in reverse complement -b, --basename Prepend the file basename to the read name --split-basename STRING Split the file basename at this character [default: .] --prefix-separator STRING Join the basename with the rest of the read name with this [default: _] -f, --frag-len INT Total fragment length [default: 500] -o, --out-prefix STR If specified, will run in paired end mode, and will output two files with this prefix, one for each end. If not specified, will output to STDOUT in single end mode. -v, --verbose Verbose output -h, --help Show this help ``` ## Input One or more FASTA or FASTQ files. By default will read from STDIN. ## Parameters Main parameters: * the desired sequence length with `--length INT` * the distance between the starting site of each read, with `--step INT` * the quality value of each base, with `--quality INT` (if you supply **-1**, the output will be in FASTA format) If processing multiple files, it can be convenient to prepend the file basename with `--basename`. The basename will be split at the first `.`, but this can be changed with `--split-basename STR/CHAR`. If a mix of forward and reverse reads is required, `--add-rc` will reverse complement every other read. If you want to test every read and its reverse complement, run the program _without_ `--add-rc` and make a reverse complement of the whole dataset with `seqfu rc`. ## Paired end mode If you specify `--out-prefix STR`, the program will run in paired end mode, and will output two files with this prefix, one for each end. The fist step is to generate a ""read"" as long as the fragment (`--frag-len`) and then the first bases (`--read-len`) will be used as the first read, and the last bases as the second read. The second read is reverse complemented ## Output The generated sequences will be printed to the standard output (STDOUT). Each read has a progressive name generated like this: * file basename (if `--basename` is specified) * a string separator (if `--basename` is specified) * the chromosome name * a string separator * a progressive number ```text @k141_1_1 GTCGGAGTCGTTTATCCGCAACATCCTGCTTGCACAGGAGTTTTATAAAAAGGAGTTCGGCATCAAGTCGAAGGATATGTTCCTGCCCGACTGCTTCGGA + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII @k141_1_2 TCGGGCAGGAACATATCCTTCGACTTGATGCCGAACTCCTTTTTATAAAACTCCTGTGCAAGCAGGATGTTGCGGATAAACGACTCCGACGACGGCATGT + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII @k141_1_3 AACGACCCGAACATGCCGTCGTCGGAGTCGTTTATCCGCAACATCCTGCTTGCACAGGAGTTTTATAAAAAGGAGTTCGGCATCAAGTCGAAGGATATGT + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII @k141_1_4 CGACTTGATGCCGAACTCCTTTTTATAAAACTCCTGTGCAAGCAGGATGTTGCGGATAAACGACTCCGACGACGGCATGTTCGGGTCGTTGGCCTCGAAC + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII @k141_1_5 CGGGGGCTTCGTTCGAGGCCAACGACCCGAACATGCCGTCGTCGGAGTCGTTTATCCGCAACATCCTGCTTGCACAGGAGTTTTATAAAAAGGAGTTCGG + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII ``` ## Shotgun simulation If you need to simulate a whole genome shotun, you will need alternative software like [ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm). ","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-orf.md",".md","4340","132","--- layout: default title: fu-orf parent: Utilities --- # fu-orf Extraction of ORFs from raw reads datasets (and other sequence files). Open reading frames are defined as a stretch of aminoacids not interrupted by stop codons: this program does not perform any _gene finding_ procedure and merely extracts ORFs (under the assumption that, running on raw reads, fragments are expected). A major update was introduced with version **1.8.4**, with improved reporting (strand and reding frame in the output), improved tests and `--scan-reverse` option (previously enabled by default). ```text fu-orf Extract ORFs from Paired-End reads. Usage: fu-orf [options] fu-orf [options] -1 File_R1.fq fu-orf [options] -1 File_R1.fq -2 File_R2.fq fu-orf --help | --codes Input files: -1, --R1 FILE First paired end file -2, --R2 FILE Second paired end file ORF Finding and Output options: -m, --min-size INT Minimum ORF size (aa) [default: 25] -p, --prefix STRING Rename reads using this prefix -r, --scan-reverse Also scan reverse complemented sequences -c, --code INT NCBI Genetic code to use [default: 1] -l, --min-read-len INT Minimum read length to process [default: 25] Paired-end optoins: -j, --join Attempt Paired-End joining --min-overlap INT Minimum PE overlap [default: 12] --max-overlap INT Maximum PE overlap [default: 200] --min-identity FLOAT Minimum sequence identity in overlap [default: 0.80] Other options: --codes Print NCBI genetic codes and exit --pool-size INT Size of the sequences array to be processed by each working thread [default: 250] --verbose Print verbose log --debug Print debug log --help Show help ``` ## Example usage Single input file (FASTA or FASTQ): ```bash fu-orf --min-size 500 data/orf.fa.gz ``` Paired-end Illumina reads: ```bash fu-orf --min-size 29 -1 data/illumina_1.fq.gz -2 data/illumina_2.fq.gz ``` will produce a FASTA output reporting, as comment, the frame and the total ORFs printed for each sequence: ```text >filt.1_1 frame=+0 tot=5 RNLIILKMDFFFENFALVGLLYGACQRLNSTKFYLMSTDYLIVKTFNNGSLGSRIDEERS >filt.1_2 frame=+2 tot=5 WSFRGSKSRNKVSVGEPAEGSLKKFNNFENGFFF >filt.1_3 frame=+2 tot=5 KLCFGRPSIWGLPEVKLNQILFNVNRLFNSQNFQQRISWFSHR >filt.1_4 frame=-1 tot=5 NLVEFNLWQAPYRRPTKAKFSKKKSIFKIIKFL >filt.1_5 frame=-2 tot=5 LLNNRLTLNKIWLSLTSGRPHIEGLPKQSFQKKNPFSKLLNFFNDPSAGSPTETLLRLLLPLNDQ >filt.2_1 frame=+0 tot=5 TYNQFFINLSHQIITNSQNFQQRISWFSHRNA >filt.2_2 frame=+1 tot=5 NKLALAVGPACRQRSKLTTNFLSTCHTRLLLIVKTFNNGSLGSRIETQ >filt.2_3 frame=+2 tot=5 WSFRGSKSRNKVSVGEPAEGSLLICLIAPHVFFFETNLLWRWAQPAARGLNLQPIFYQLVTPDYY >filt.2_4 frame=-1 tot=5 KIGCKFRPLAAGWAHRQSKFVSKKNTCGAIKQISNDPSAGSPTETLLRLLLPLNDQ >filt.2_5 frame=-2 tot=5 QVDKKLVVSLDLWRQAGPTAKASLFQRKTHVVQLSKSVMILPQVHLRKPCYDFYFL ``` ## Genetic codes Genetic codes can be changed using [NCBI Genetic Codes](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). Type `fu-orf --codes` to print the following list. * `1`: The Standard Code * `2`: The Vertebrate Mitochondrial Code * `3`: The Yeast Mitochondrial Code * `4`: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code * `5`: The Invertebrate Mitochondrial Code * `6`: The Ciliate, Dasycladacean and Hexamita Nuclear Code * `9`: The Echinoderm and Flatworm Mitochondrial Code * `10`: The Euplotid Nuclear Code * `11`: The Bacterial, Archaeal and Plant Plastid Code * `12`: The Alternative Yeast Nuclear Code * `13`: The Ascidian Mitochondrial Code * `14`: The Alternative Flatworm Mitochondrial Code * `16`: Chlorophycean Mitochondrial Code * `21`: Trematode Mitochondrial Code * `22`: Scenedesmus obliquus Mitochondrial Code * `23`: Thraustochytrium Mitochondrial Code * `24`: Rhabdopleuridae Mitochondrial Code * `25`: Candidate Division SR1 and Gracilibacteria Code * `26`: Pachysolen tannophilus Nuclear Code * `27`: Karyorelict Nuclear Code * `28`: Condylostoma Nuclear Code * `29`: Mesodinium Nuclear Code * `30`: Peritrich Nuclear Code * `31`: Blastocrithidia Nuclear Code * `33`: Cephalodiscidae Mitochondrial UAA-Tyr Code","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-sw.md",".md","2475","75","--- layout: default title: fu-sw parent: Utilities --- # fu-sw Simple implementation of the _Smith-Waterman_ alignment: ```text Usage: fu-sw [options] -q QUERY -t TARGET Options: -q --query File with the sequence(s) to align against target -t --target File with the target sequence(s) -i --id ID Align only against the sequence named `ID` in the target file -s --showaln Show graphical alignment Smith-Waterman options: --score-match INT Score for a match [default: 10] --score-mismatch INT Score for a mismatch [default: -5] --score-gap INT Score for a gap [default: -10] --min-score INT Minimum alignment score [default: 80] --pct-id FLOAT Minimum percentage of identity [default: 85] Other options: --pool-size INT Number of sequences/pairs to process per thread [default: 20] -v --verbose Verbose output -h --help Show this help ``` ## Input files Input files can be in FASTA or FASTQ format, and both query and target can hold multiple sequences even if the common application is to have a single sequence in the target file. If the target file contains multiple sequences but only one is the intended target, the target can be specified with `--id` parameter. ## Example output The output will print the alignment score and coordinates in a single line after `QUERY` and `TARGET`. If `--showaln` is specified, a graphical summary of the local alignment is provided. ```text # QUERY: not_in_target ## TARGET: ecoli # QUERY: 16S_1_for_ins ## TARGET: ecoli Score: 406 (97.18%) Length: 69 Strand: + Query: 0-71 Target: 21-90 GCTCAGATTGAACGCTccGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGC |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| GCTCAGATTGAACGCT--GGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGC # QUERY: 16S_2_rev ## TARGET: ecoli Score: 312 (100.00%) Length: 52 Strand: - Query: 0-52 Target: 175-227 CGCATAATGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGG |||||||||||||||||||||||||||||||||||||||||||||||||||| CGCATAATGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGG ``` ## Release note From 1.19.0 the algorithm has been rewritten using only standard libraries, while the initial implementation used the neo library for storing matrices. This resulted in a 2X speedup. ","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-tabcheck.md",".md","1597","69","--- layout: default title: fu-tabcheck parent: Utilities --- # fu-tabcheck An utility to parse CSV/TSV files to check that all the records have the same size. Multiline records are supported using double quotes as field delimiter. Gzipped files are also supported. ``` fu-tabcheck A program inspect TSV and CSV files, that must contain more than 1 column. Double quotes are considered field delimiters, if present. Gzipped files are supported natively. Usage: fu-tabcheck [options] ... Options: -s --separator CHAR Character separating the values, 'tab' for tab and 'auto' to try tab or commas [default: auto] -c --comment CHAR Comment/Header char [default: #] --verbose Enable verbose mode ``` ## Output Tabular output has these columns: * File name * Pass/Error * Columns number * Records number * Separator (when using _auto_ both tabs and commas are tested) Example: ``` data/tab.txt.gz Pass 8 7 separator= data/tab.txt Pass 4 3 separator= data/tab-multi.tsv Pass 2 4 separator= data/table.csv Pass 3 3 separator=, data/table.tsv Pass 3 4 separator= data/table2.tsv Error data/tablegz.tsv.gz Pass 3 4 separator= ``` :bulb: Multiline records are supported using double quotes, like: ```text #ID Description R01 ""this is a cell with a tab inside!"" R02 ""this is a multi-line description"" R03 Last Record ``` ## Exit code A single file is not a valid table will lead to non-zero exit status.","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-index.md",".md","1105","48","--- layout: default title: fu-index parent: Utilities --- # fu-index Extracts the index (barcode) from Illumina demultiplexed files. ```text Fastx utility A program to print the Illumina INDEX of a set of FASTQ files Usage: fu-index [options] ... Options: -m, --max-reads INT Evaluate INT number of reads, 0 for unlimited [default: 8000] -r, --min-ratio FLOAT Minimum ratio of matches of the top index [default: 0.90] -h, --header Add header to output --verbose Print verbose log --help Show help ``` ## Input files FASTQ files demultiplexed by CASAVA (Illumina). ## Example output A tabular output contains: * filename * extracted tag * fraction of the top tag (accounts for errors) * PASS (""PASS"" or ""--"") if the top tags is >= min-ratio * Instrument code (from 1.12) * Run number (from 1.12) * Flowcell ID (from 1.12) ``` data/illumina_1.fq.gz TACGCTGC+CTATTAAG 1.00 PASS A00709 43 HYG25DSXX data/illumina_2.fq.gz TACGCTGC+CTATTAAG 1.00 PASS A00709 43 HYG25DSXX ```","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-virfilter.md",".md","1987","59","--- layout: default title: fu-virfilter parent: Utilities --- # fu-virfilter Filter sequences from VirFinder predictions CSV file. ```text Usage: fu-virfilter [options] Files: VirFinder output file (csv format) FASTA file to filter Options: -p, --max-pvalue FLOAT Maximum p-value to keep [default: 0.05] -s, --min-score FLOAT Minimum score [default: 0.90] --min-len INT Minimum length [default: 100] --max-len INT Maximum length [default: 1000000] Other options: --sep CHAR Separator [default: ,] -v, --verbose Verbose output -h, --help Show this help ``` ## Example input and output Virfinder output: ``` """",""name"",""length"",""score"",""pvalue"" ""1"",""k141_48132 flag=1 multi=2.0000 len=317"",317,0.805265057231112,0.003813306852036 ""2"",""k141_58828 flag=1 multi=1.0000 len=302"",302,0.386511266211445,0.27648460774578 ""3"",""k141_80217 flag=1 multi=2.0000 len=310"",310,0.245554967660862,0.424905660377358 ``` While the FASTA file is: ``` >k141_74870 flag=1 multi=2.0000 len=369 AAAGGCGTGTGTGCCTTGAGCCTTAGACCATGTGAATTGTAAATCAGTGTATAGCCGGCGATACCGGTTTTCTTGTTCA TCGCACGGCAGAAGCCTCCATCTATCACAAACAGCTTGCCATTGGCCCTGACAGGGTTCTCTCCCTCTATTGCGTGAAC GGTGTATGTCCATTTATGATATGCGCATCATCATCATACAGCCCGAACTCGTGCAGTATCTGACAGCAGAAGCTCTTAT CGTAATACCTGCTGTAATATGGGTTAGAAGGCTCTTCCCACATGCTCTTGTCTGTAACATATTCCATCTCAAAGGTCTT AAGCCTTCTGCCGCACAGCGGTGATTTTTCTCCTCCCCACAAAAACCACATA >k141_106952 flag=1 multi=2.0000 len=384 GCGGGCGTTACCCCGGAAGCGGCATGGAGGGCCTGGGAGAAACCGTCCCACAGGCTGCGGCTGCAGCGGCAGTCCGCGA GGGAGACCGGATACCAGCGGACCAGGGGGTCGGCCGCGACGCGCCGCCCGGTCCCGCCGGTGAGGATGCGCAGCCCCCC GGATTCTGCGGGCAGGCGGACCTCCAGATCTTCCGTGACCGGGGTCTGACAGGCCAGGACCGAGACCCATTCCTCCCCG CGGCGGAGCGCCACACGGCACTTTCCGCAGGTCCCATTCCCGCCGCAGGGGCTGTCCAGCCAGAGACCGGCCGCACGGC AGGCCTCCATCAGCGTGCTTCCCAGGGGGACGGAGCAGCGCACGTCCGCCGGGAGAAAGCGTACCTGT ```","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-homocomp.md",".md","704","41","--- layout: default title: fu-homocom parent: Utilities --- # fu-homocom Remove all the homopolymers from FASTA and FASTQ files. The output format is the same of the input. ```text Usage: fu-homocompress [options] [...] Other options: --pool-size INT Number of sequences to process per thread [default: 50] --max-threads INT Maxiumum number of threads to use [default: 4] -v, --verbose Verbose output -h, --help Show this help ``` ## Example input and output ``` @polya ACGTACACGTGACGAAAAAAAAAAAAAACGT + IIIIIIIIIIIIIII!!!!!!!!!!!!!III ``` will be printed as ``` @polya ACGTACACGTGACGACGT + IIIIIIIIIIIIIIIIII ```","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-16Sregion.md",".md","3655","124","--- layout: default title: fu-16Sregion parent: Utilities --- # fu-16Sregion ```note This utility is still in development, but feedback is welcome. ``` Align paired-end, or single-end, reads against a 16S reference sequence to determine the hypervariable regions sequences via local alignment. Can read one FASTA/FASTQ file or data from standard input. ```text Usage: fu-16Sregion [options] [] Options: -r --reference FILE FASTA file with a reference sequence, E. coli 16S by default -j --regions FILE Regions names in JSON format, E. coli variable regions by default -m --min-fraction FLOAT Minimum fraction of reads classified to report a region as detected [default: 0.5] --min-score INT Minimum alignment score (approx. %id * readlen * matchScore) [default: 2000] --max-reads INT Parse up to INT reads then quit [default: 500] Smith-Waterman: --score-match INT Score for a match [default: 10] --score-mismatch INT Score for a mismatch [default: -5] --score-gap INT Score for a gap [default: -10] Other options: --pool-size INT Number of sequences/pairs to process per thread [default: 25] -v --verbose Verbose output --debug Enable diagnostics -h --help Show this help ``` ## Example output A tabular report, per read, is provided with the following columns * Read name * Primary target region * Alignment score * Region of the reference sequence covered (coordinates) The **main** output is given as two columns: * regions detected in the same read (e.g. ""V3,V4"") * fraction of reads with the combination Example: ```text V3-V4 0.83 ``` This is only reported when the number of reads / total reads is above `--min-fraction`. When activating the `--verbose` switch, some more information will be printed to the standard error, but also a **read by read output** will be printed (read name, score, target region covered, detected regions and Pass/Fail): ```text M05517:39:000000000-CNNWR:1:1105:7840:22808 score:2955 alignment:340..805 regions:V3,V4 Pass M05517:39:000000000-CNNWR:1:1105:24801:23102 score:3480 alignment:340..805 regions:V3,V4 Pass M05517:39:000000000-CNNWR:1:1105:9773:23284 score:2835 alignment:340..805 regions:V3,V4 Pass M05517:39:000000000-CNNWR:1:1105:9791:23288 score:2835 alignment:340..805 regions:V3,V4 Pass M05517:39:000000000-CNNWR:1:1105:11642:23566 score:1650 alignment:NA regions: Fail M05517:39:000000000-CNNWR:1:1105:13198:23694 score:1535 alignment:NA regions: Fail M05517:39:000000000-CNNWR:1:1105:15837:23728 score:2240 alignment:340..641 regions:V3,V4 Pass M05517:39:000000000-CNNWR:1:1105:14501:23779 score:2225 alignment:340..641 regions:V3,V4 Pass ``` ## Example use with paired-reads To check paired-end reads, they can be processed independently or merged (if they overlap) before. SeqFu merge can be used for this purpose: ``` seqfu merge -1 read_R1.fq -2 read_R2.fq | fu-16region ``` ## Region names By default the following regions are used, but a new set can be fed in JSON format (each region should contain the `start` and `end` values as show in the example) ```json { ""V1"": { ""start"": 68, ""end"": 99 }, ""V2"": { ""start"": 136, ""end"": 242 }, ""V3"": { ""start"": 338, ""end"": 533 }, ""V4"": { ""start"": 576, ""end"": 682 }, ""V5"": { ""start"": 821, ""end"": 879 }, ""V6"": { ""start"": 970, ""end"": 1046 }, ""V7"": { ""start"": 1117, ""end"": 1294 }, ""V8"": { ""start"": 1435, ""end"": 1465 } } ```","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-cov.md",".md","1737","59","--- layout: default title: fu-cov parent: Utilities --- # fu-cov A program to filter the output of assembly programs using the coverage information they print in the sequence names. ```text Extract contig by sequence length and coverage, if provided in the sequence name. Usage: fu-cov [options] [inputfile ...] Arguments: [inputfile ...] Options: -h, --help -v, --verbose Print verbose messages -s, --sort Store contigs in memory, and sort them by descending coverage -c, --min-cov=MIN_COV Minimum coverage (default: 0.0) -l, --min-len=MIN_LEN Minimum length (default: 0) -x, --max-cov=MAX_COV Maximum coverage (default: 0.0) -y, --max-len=MAX_LEN Maximum length (default: 0) -t, --top=TOP Print the first TOP sequences (passing filters) when using --sort (default: 10) ``` ## Input The FASTA output of an assembly program (currently tested with SPAdes, MegaHit, Unicycler, Shovill), as the _length_ of the sequences is clearly checked from the FASTA file itself, while the coverage is found in the sequence description: Example of contig name from _Shovill_: ``` >contig00001 len=596929 cov=9.9 corr=0 origname=NODE_1_length_596929_cov_9.873201_pilon sw=shovill-spades/1.0.4 date=20181128 ACCCGGTAGAATACCGGACTGAGTATCAAAAAGCCGGTTAACTGAAACTGTCCAGGTTTTGGGGTTCAGTTCATGCCGCATCTTATCCGACCTTGTATTATCCCTCCAGTGCAGAGAAAATC ... ``` ## Output A set of filtered contigs in FASTA file. Will print to STDERR a summary like: ```` 1/1 sequences printed (1 with coverage info) from 1 files. Skipped: 0 too short, 0 too long, then 0 low coverage, 0 high coverage, . Average length: 180.00 bp, [180.0 - 180.0] Average coverage: 9.90X, [9.9-9.9] ```","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-msa.md",".md","3841","125","--- layout: default title: fu-msa parent: Utilities --- # fu-msa ```note Preliminary version ``` Interactive **multiple sequence alignment** viewer from the Command Line. ![Multiple sequence aligner]({{site.baseurl}}/img/msa.png) ```text Usage: full [options] Keys: Scroll Horizontally Left and Right arrow By 10 bases L, K By 100 bases ShiftL, ShiftK To the beginning 1 To middle parts 2..9 To the end 0 Scroll Vertically A, Up Arrow/ Z, Down Arrow Jump to top ShiftA, PageUp Jump to bottom ShiftZ, PageDown Rotate color scheme Tab Refresh screen F5 Resize seq labels -,+ Search / (seqname, "":INT"", ""#SEQ"") Quit Q, CtrlC Options: -m, --mouse Enable mouse -n, --norefresh Disable autorefresh -j, --jumpsize INT Jump size (big jump is 10X) [default: 10] Visualization settings: -i, --seqindex INT Start visualization at this sequence [default: 0] -p, --seqpos INT Start visualization at this nucleotide [default: 0] -w, --label-width INT Sequence label width [default: 20] -s, --setting-string STR Settings string (overrrides all other settings) is in the format Seq:{seqindex}:{seqpos}:{labelwidth} and is the return value of the program when it is closed. More documentation online at https://telatin.github.io/seqfu2/ ``` ## Keyboard #### Horizontal scrolling * :arrow_left:, :arrow_up: : scroll by one nucleotide * `K`, `L`: scroll left and right respectively, by 10 nucleotides * `Shift + K`, `Shift + L`: scroll left and right respectively, by 100 nucleotides * `End`: Move to sequence end * `Home`: Move to the beginning of the sequence * `1`: Move to the first base * `2`..`9`: Move to 20% .. 90% of the sequence * `0`: Move to the last base #### Vertical scrolling * `A`, `Z` and :arrow_up:, :arrow_down: : Move up and down by one sequence * `Shift + A`, `Shift + Z`: Move to top and move to bottom #### Search * `/` Trigger search, then: * Type the query * Hit `Enter` to submit or `Esc` to abort * The query can be: * part of a sequence name * `:` followed by a sequence index (eg: `:0` to go to the first sequence) * `#` followed by a sequence (eg: `#ATTAC` to jump to the position of the first occurrence of ATTAC) #### Visualization * `Space`: toggle consensus sequence from ""Consensus"" (show bases identical across all the sequences) to ""Majority"" (show bases shared by 50% of the sequences or more) * `Tab`: toggle color scheme * `-`,`+`: Decrease and increase by one the sequence label width * `F5`, `R`: refresh * `F6`: toggle autorefresh on/off * `H`: toggle help screen (only major keys are reported) #### Mouse * `M`: toggle mouse on/off * When mouse is on: * Click in a nucleotide to set that position as first (scroll right) * Click to the sequence name area (left) to scroll left ### Resuming session When pressing quit (`Q`) the program will print a configuration string like: `Seq:0:6:20` that can be used to resume the session at the same position with: ```bash fu-msa {input_file} --setting-string Seq:0:6:20 ``` The settings string is in the format `Seq:{seqindex}:{seqpos}:{labelwidth}` ### Colors * DNA: `A` (red), `C` (cyan), `G` (green), `T` (yellow) * Protein: [""Lesk"" scheme](https://www.bioinformatics.nl/~berndb/aacolour.html): * Hydrophobic, green * Small non polar, yellow (should be orange) * Polar, magenta * Negative charge, red * Positive charge, cyan (should be blue) ### Screenshot ![Screenshot of ""seqfu MSA view""]({{site.baseurl}}/img/screenshot-fu-msa.svg ""SeqFu MSA view"")","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-nanotags.md",".md","3685","93","--- layout: default title: fu-nanotags parent: Utilities --- # fu-nanotags ```note Experimental utility. Feedback for this tool is welcome. ``` Search for tags (one or more sequences) in long reads using _Smith-Waterman_ alignment. The tag has to be at the beginning of the read (specifying the region to scan with `--cut INT`) or at the end (revserse complemented). If `--cut=0` the search is in the full read. ```text Usage: fu-nanotags [options] -q QUERY [...] Options: -q, --query TAGSEQ Sequence string OR file with the sequence(s) to align against reads -s, --showaln Show graphical alignment -c, --cut INT Cut input reads at INT position [default: 300] -x, --disable-rev-comp Do not scan reverse complemented reads Alignment options: -i, --pct-id FLOAT Percentage of identity in the aligned region [default: 80.0] -m, --min-score INT Minimum alignment score (0 for auto) [default: 0] Smith-Waterman parameters: -M, --weight-match INT Match [default: 5] -X, --weight-mismatch INT Mismatch penalty [default: -3] -G, --weight-gap INT Gap penalty [default: -5] Other options: --pool-size INT Number of sequences/pairs to process per thread [default: 25] -v, --verbose Verbose output -h, --help Show this help ``` ## Output The program will print to the **standard output** the reasd containing the tag, under the specified alignment criteria. A comment will be added to the reads specifying which tag was found (e.g. `tags=tag1;tag4`). The program will print to the **standard error** the number of passing reads per file processed, and the grand total. Example: ```text tradis/fastq_1.fq 60.00% (18/30) sequences printed, of which 8 in reverse strand. tradis/fastq_2.fq.gz 53.75% (2150/4000) sequences printed, of which 949 in reverse strand. Total 53.80% (2168/4030) sequences printed, of which 957 in reverse strand. ``` ## Optimisation If the tag is 100 bp long and we expect to be at the very beginning (or end) of the read, it's advisable to reduce the `--cut INT` parameter accordingly to speedup the alingment step (for example, to 110, to account for a small variation). The current version of the program is single threaded, but a multithreading application will be released. ## Example ```bash fu-nanotags -q tag.fa fastq-reads.fq.gz > passed.fq ``` To inspect the parameters, add `--verbose --showaln`, possibly redirecting the output to `less -S` for a preliminary inspection: ```bash fu-nanotags -q tag.fa reads.fq.gz --verbose --showaln 2>&1 | less -S ``` A fraction of the output is like the following: ``` # a564e10b-c82e-4e59-98a4-fdc6f1b31acb:test-tag strand=-;score=167;pctid=94.57% < AATGATA-TGCGACCACTGAGATCTACACCTCTCTATACACTC-TT-CCTACACGACGCTCTTCCGATCTTTCGTACGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTG < ||||||| |||||||| ||||||||||||||||||||||||| || |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < AATGATACGGCGACCACCGAGATCTACACCTCTCTATACACTCTTTCCCTACACGACGCTCTTCCGATC--TCGTACGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTG # 132518b1-1522-45ed-9a77-94a3c981ac20:test-tag strand=+;score=531;pctid=90.55% > AATGATACGGCGACCACCGAGATCTACACTATCCCTCTACACTCTTTCCCTACACGACGCTCTTCCGATCTACGTACGTGAGTTTAAATGT-GTTAGCTAAGGTGTATAT-AGCTTCCGACTTCAGC > ||||||||||||||||||||||||||||| || || |||||||||||||||||||||||||||||||||| ||||||||||||||||||| || |||||||||||| | | |||||||||||| | > AATGATACGGCGACCACCGAGATCTACAC-CTCTCTATACACTCTTTCCCTACACGACGCTCTTCCGATCT-CGTACGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAAC ```","Markdown" "Bioengineering","telatin/seqfu2","docs/utilities/fu-multirelabel.md",".md","1166","39","--- layout: default title: fu-multirelabel parent: Utilities --- # fu-multirelabel A program to rename sequences from multiple files (adding the filename, and or numerical postfix). Will fail if multiple sequence receive the same name. ```text Usage: fu-multirelabel [options] FILE... Options: -b, --basename Prepend file basename to sequence -r, --rename NAME Replace original name with NAME -n, --numeric-postfix Add progressive number (reset at each new basename) -t, --total-postfix Add progressive number (without resetting at each new input file) -d, --split-basename CHAR Remove the final part of basename after CHAR [default: .] -s, --separator STRING Separator between prefix, name, suffix [default: _] --no-comments Strip out comments --comment-separator CHAR Separate comment from name with CHAR [default: TAB] ``` ## Description A list of files (can be specified with wild chars) that can contain sequences with the same name. The program allows to prepend the filename as prefix. ## Example usage ```bash fu-multirelabel -b *.fasta > relabeled.fasta ```","Markdown" "Bioengineering","telatin/seqfu2","docs/releases/history.md",".md","5508","199","--- layout: default title: History parent: Releases --- ## Release history ### version 1.22 * Added `seqfu cat --anvio` * Added layouts to `seqfu metadata`, now supporting nf-core/rnaseq and nf-core/ampliseq * Improved `seqfu derep` ### version 1.20 * Improved `seqfu interleave/deinterleave` * Migration to Nim 2.0 * Added `--translate` to `fu-orf` * Faster smith-waterman `fu-sw` ### version 1.18 * Added paired end support to `fu-shred` ### version 1.17 * Bugfixes and removal of thread library ### version 1.16 * Added amino-acid color scheme for `fu-msa` * Bugfixes in `seqfu check` and `seqfu bases` ### version 1.15.0 * New SeqFu check program to validate the integrity of FASTQ datasets * Bug fix in seqfu qual that was printing debug information in non-debug runs #### 1.15.3 * Added SeqFu bases to evaluate the composition of FASTX files ### version 1.14.0 * **Seqfu grep** will die if fed with non existing files (to ensure no wrong parameters were passed) * **Seqfu grep** will match oligos case insensitive by default * Addedd invert match `-v` to `seqfu grep` * Improved `fu-tabcheck`, notably added `--inspect` option to print columns info * `fu-split` now can use a different SeqFu than specified in path, setting `$SEQFU_BIN` or `--bin` option * `fu-split` version check fixed * :warning: Bugfix in `seqfu tab`: was not working with FASTA files ### version 1.13.0 * `seqfu cat` now can skip a set of initial sequences (`--skip-first INT`) or start from a specific sequence (`--jump-to`) * Minor updates in the test suite, github actions (including rich_codex) and documentation updates #### 1.13.1 * added `fu-split` (experimental) #### 1.13.2 * added `--print-last` option to **seqfu cat** and **seqfu heda** * updated `fu-split`, with support for paired end reads, improved performance thanks to `--print-last`, new tests ### version 1.12.0 * Expanded ""fu-index"": also reports run infos, not only indexes * Minor bugfix ### version 1.11.0 * Improved seqfu stats: added sorting option and JSON output, added GC content, improved test suite. * bugfix Seqfu tabulate -d (detabulate) was too stringent in requiring forward and reverse reads to have the same length 🤦 ### version 1.10.0 * Added support for MetaPhage to seqfu metadata * Added --header to fu-tabcheck * Minor fixes ### version 1.9.3 * bugfix: seqfu cat controls the length of operations (truncate, trim) * improved: seqfu cat improved renaming options (basename and strip-name will now add a progressive number automatically) ### version 1.9.2 * Bugfix on Seqfu Detabulate ### version 1.9.1 * Fixes #8 * This is a re-release finally with all the necessary commits ### version 1.9.0 * seqfu grep now has -w (word) and -f (full) match options. default behaviour unchanged. * seqfu cat now has a filter for Ns (--max-ns INT) * seqfu cat now has a filter for the total expected errors (--max-ee FLOAT), and can report --add-ee and --add-initial-ee * Added header line in seqfu metadata when using ""irida"" formats ### version 1.8.6 * Enabled **seqfu rotate** ### version 1.8.4 * **fu-orf** * Fixed bug in `fu-orf` to allow for single sequences * Introduced `-r`, `--scan-reverse` to include reverse complement in the ORF finder * `fu-orf` also prints frame in the sequence comment * Expanded test suite ### version 1.8.3 * Markdown documentation improvements * Splashscreen for *fu-virfilter* fixed * Argument parser for _fu-cov_ improved * Now `seqfu --version` and `seqfu version` will print the version number and exit * Added test for _fu-cov_ * Added citation in main command and repository ### version 1.8.2 * Added `fu-virfilter` to filter VirFinder results * Bugfix in `seqfu cat --basename`: the last update made it working only when prefix was also specified ### version 1.8.1 * introduced `fu-homocomp` to compress homopolymers ### version 1.8.0 * added `seqfu list` to extract sequences via a list ### version 1.7.2 * `seqfu grep` supports for comments ### version 1.7.1 * **Bugfix release**: `seqfu cat` with no parameters was stripping the reads name ### version 1.7.0 * Default primer character for oligo matches in seqfu view was Unicode, now Ascii * Updated `seqfu cat` with improved sequence id renaming handling * Updated `seqfu grep` to report the _oligo_ matches in the output as sequence comments ### version 1.6.3 * Removed ambiguity on `-q` in `seqfu head` * Minor documentation updates ### version 1.6.0 * Improved STDIN messages, that can be disabled by `$SEQFU_QUIET=1` * Added `--format irida` in `seqfu metadata` (for [IRIDA uploader](https://github.com/phac-nml/irida-uploader)) * Added `--gc` in `seqfu qual`: will print an additional column with the GC content * Minor improvements on `seqfu cat` ### version 1.5.4 * Improved STDIN messages, that can be disabled by `$SEQFU_QUIET=1` * Minor improvements on `seqfu cat` ### version 1.5.2 * **seqfu cat** has new options to manipulate the sequence name (like `--append STRING`) and to add comments (like `--add-len`, `--add-gc`) ### version 1.5.0 * **seqfu count** now multithreading and redesigned. The output format is identical but the order of the records is not protected (use **seqfu count-legacy** if needed) * **seqfu cat** can print a list of sequences matching the criteria (`--list`) ### version 1.4.0 * Added **fu-shred** * Added `--reverse-read` to *fu-nanotags* # version 1.3.6 * Automatic release system * Documentation updates * Minor updates ","Markdown" "Bioengineering","telatin/seqfu2","docs/scripts/fu-pecheck.md",".md","959","41","--- layout: default title: fu-pecheck parent: Helper Utilities --- # fu-pecheck ```note Preliminary version ``` A program to check the integrity of Paired End FASTQ files. ```text usage: fu-pecheck [-h] [--for-tag FOR_TAG] [--rev-tag REV_TAG] [--verbose] [--version] DIR Validate FASTQ files positional arguments: DIR Input directory optional arguments: -h, --help show this help message and exit --for-tag FOR_TAG Tag to use for the forward reads output (default: _R1) --rev-tag REV_TAG Tag to use for the forward reads output (default: _R2) --verbose Verbose output --version show program's version number and exit ``` This script runs `fu-secheck` twice and compare the results, and will print a five column table with the following columns: 1. Sample basename 2. Status (`OK` or `ERR`) 3. Number of reads or ""None"" if the file is corrupt 4. Name of the first read 5. Name of the last read ","Markdown" "Bioengineering","telatin/seqfu2","docs/scripts/fu-split.md",".md","3185","79","--- layout: default title: fu-split parent: Helper Utilities --- # fu-split ```note Preliminary version ``` Split a FASTQ or FASTA files into multiple files, by: * Number of desired output files (`--num-files INT`) * Number of (max) sequences per file (`--num-seqs INT`) * Number of (max) bases per file (`--num-bases INT`) An important component to configure the program is the ""output file"" string, see below. ```text usage: fu-split [-h] -i INPUT [-I INPUT_REV] -o OUTPUT [--for-tag FOR_TAG] [--rev-tag REV_TAG] (-n NUM_FILES | -s NUM_SEQS | -b NUM_BASES) [--threads THREADS] [--number-char NUMBER_CHAR] [--compress] [--verbose] [--debug] [--version] Split FASTA/FASTQ files into multiple files optional arguments: -h, --help show this help message and exit -i INPUT, --input INPUT Input file -I INPUT_REV, --input-rev INPUT_REV Second input file (reverse pair) -o OUTPUT, --output OUTPUT Output file (add a stretch of 3+ zeroes to specify the progressive number), compression will be detected. Example: parz_0000.fq.gz --for-tag FOR_TAG Tag to use for the forward reads output (default: _R1 --rev-tag REV_TAG Tag to use for the forward reads output (default: _R2 -n NUM_FILES, --num-files NUM_FILES Number of desired files -s NUM_SEQS, --num-seqs NUM_SEQS Number of sequences per file -b NUM_BASES, --num-bases NUM_BASES Number of bases per file --version show program's version number and exit Other options: --threads THREADS Number of threads (-n only) [default: 8 --number-char NUMBER_CHAR Character used to represent the progressive number in output string [default: 0 --compress Force compression of the output files --verbose Verbose mode --debug Debug mode ``` ## Output file string The ideal way to use `fu-split` is to use the `--output` option to specify the output file format with this apprach: *prefix*, *progressive number*, *suffix*, where *progressive number* is a stretch of zeroes as long as you would like the progressive number (zeroes can be changed with `--number-char`). Example: * `--output parz_0000.fq.gz`: forces output in FASTQ format, compressed with Gzip, with four digits of progressive number. * `--output parz_000.fa`: forces output in FASTA format, uncompressed, with three digits of progressive number. * `--output parz`: missing the *progressive number* part, this will be used as prefix, with a four digits progressive number (not recommended, behaviour can change in the future) ## Paired end Specify both `--input` and `--input-rev` to split a paired end FASTQ file. The output file will be differentiated with the `--for-tag` and `--rev-tag` options (default: `_R1` and `_R2`). ## Binary Export `$SEQFU_BIN` to specify the path to SeqFu, otherwise will default to `seqfu` (as in `$PATH`). ## Splashscreen ![Screenshot of ""seqfu split""]({{site.baseurl}}/img/screenshot-fu-split.svg ""SeqFu split"")","Markdown" "Bioengineering","telatin/seqfu2","docs/_scripts/add_frontmatter.py",".py","2632","95","#!/usr/bin/env python3 """""" Add front matter to markdown files for Jekyll navigation. This script adds proper front matter to child pages in the tools, utilities, and scripts directories. """""" import os import re from pathlib import Path # Configuration BASE_DIR = Path(__file__).parent.parent SECTIONS = { 'tools': 'Core Tools', 'utilities': 'Utilities', 'scripts': 'Helper Utilities', 'releases': 'Releases' } def has_frontmatter(content): """"""Check if file already has front matter."""""" return content.strip().startswith('---') def extract_title_from_content(content): """"""Extract title from the first # heading in the content."""""" lines = content.split('\n') for line in lines: if line.strip().startswith('# '): return line.strip()[2:].strip() return None def create_frontmatter(title, parent): """"""Create front matter block."""""" return f""""""--- layout: default title: {title} parent: {parent} --- """""" def process_file(filepath, parent_name): """"""Add front matter to a single file."""""" with open(filepath, 'r', encoding='utf-8') as f: content = f.read() # Skip if already has front matter if has_frontmatter(content): print(f""Skipping {filepath} (already has front matter)"") return False # Extract title from content title = extract_title_from_content(content) if not title: print(f""Warning: Could not find title in {filepath}"") # Use filename as fallback title = filepath.stem.replace('-', ' ').replace('_', ' ').title() # Create new content with front matter frontmatter = create_frontmatter(title, parent_name) new_content = frontmatter + content # Write back to file with open(filepath, 'w', encoding='utf-8') as f: f.write(new_content) print(f""Added front matter to {filepath}"") return True def main(): """"""Process all markdown files in the specified sections."""""" processed = 0 for section_dir, parent_name in SECTIONS.items(): section_path = BASE_DIR / section_dir if not section_path.exists(): print(f""Warning: Directory {section_path} does not exist"") continue print(f""\nProcessing {section_dir}/ (parent: {parent_name})"") # Process all .md files except README.md for md_file in section_path.glob('*.md'): if md_file.name.upper() == 'README.MD': continue if process_file(md_file, parent_name): processed += 1 print(f""\n\nTotal files processed: {processed}"") if __name__ == '__main__': main() ","Python" "Bioengineering","telatin/seqfu2","scripts/makeFileFeatures.py",".py","491","19","#!/usr/bin/env python """""" A Python 3.6+ compatible script to generate FASTA or FASTQ files, randomly or using a template. """""" import argparse import random import string import sys def main(): args = argparse.ArgumentParser(description=__doc__) args.add_argument('output', help='Output file') args.add_argument('count', type=int, help='Number of sequences to generate') args.add_argument('--template', help='Template file') if __name__ == '__main__': exit(main())","Python" "Bioengineering","telatin/seqfu2","bench/bash-deinterleave.sh",".sh","233","10","#!/bin/bash if [[ $# != 3 ]] then echo ""USAGE: $0 interleaved.fastq deinterleaved.R1.fastq deinterleaved.R2.fastq"" exit 1 fi paste - - - - - - - - < ""$1"" | tee >(cut -f 1-4 | tr '\t' '\n' > ""$2"") | cut -f 5-8 | tr '\t' '\n' > ""$3"" ","Shell" "Bioengineering","telatin/seqfu2","bench/interleave.md",".md","411","6","| Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `./bin/seqfu interleave -1 R1.fq -2 R2.fq` | 4.229 ± 0.032 | 4.201 | 4.310 | 1.01 ± 0.02 | | `seqfu interleave -1 R1.fq -2 R2.fq` | 4.202 ± 0.056 | 4.168 | 4.355 | 1.00 | | `paste R1.fq R2.fq \| paste - - - - \| awk -v OFS='\n' -v FS='\t' '{print($1,$3,$5,$7,$2,$4,$6,$8)}'` | 4.699 ± 0.033 | 4.670 | 4.786 | 1.12 ± 0.02 | ","Markdown" "Bioengineering","telatin/seqfu2","bench/bash-interleave.sh",".sh","176","9","#!/bin/bash if [[ $# != 2 ]] then echo ""USAGE: $0 R1.fastq R2.fastq"" exit 1 fi paste ""$1"" ""$2"" | paste - - - - | awk -v OFS='\n' -v FS='\t' '{print($1,$3,$5,$7,$2,$4,$6,$8)}' ","Shell" "Bioengineering","telatin/seqfu2","bench/interleave_benchmarks.md",".md","262","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `seqfu interleave -1 R1.fq -2 R2.fq` | 4.706 ± 0.139 | 4.507 | 4.939 | 1.00 | | `taskset 1 ./bash_interleave.sh R1.fq R2.fq` | 11.440 ± 0.068 | 11.349 | 11.595 | 2.43 ± 0.07 | ","Markdown" "Bioengineering","telatin/seqfu2","bench/deinterleave_benchmarks.md",".md","290","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `seqfu deinterleave -o de interleaved.fq` | 3.926 ± 0.080 | 3.831 | 4.075 | 1.00 | | `taskset 1 ./bash_deinterleave.sh interleaved.fq de_R1.fq de_R2.fq` | 12.819 ± 0.098 | 12.659 | 12.952 | 3.26 ± 0.07 | ","Markdown" "Bioengineering","telatin/seqfu2","bench/run-benchmarks.md",".md","1522","56","# Benchmark script ```bash #!/bin/bash # RUN BENCHMARKS # requires hyperfine if [[ $# != 2 ]] then echo ""USAGE: $0 R1.fastq.gz R2.fastq.gz"" exit 1 fi R1=""$1"" R2=""$2"" ################# # PREPARE FILES # ################# echo Decompress test files zcat ""$R1"" > R1.fq zcat ""$R2"" > R2.fq seqfu interleave -1 R1.fq -2 R2.fq > interleaved.fq hyperfine --warmup 1 --export-markdown interleave_benchmarks.md --export-csv interleave_benchmarks.csv ""seqfu interleave -1 R1.fq -2 R2.fq"" ""taskset 1 ./bash_interleave.sh R1.fq R2.fq"" hyperfine --warmup 1 --export-markdown deinterleave_benchmarks.md --export-csv deinterleave_benchmarks.csv ""seqfu deinterleave -o de interleaved.fq"" ""taskset 1 ./bash_deinterleave.sh interleaved.fq de_R1.fq de_R2.fq"" #for i in {1..3} #do time sleep 0.1 > /dev/null #done 2>&1 | paste - - - - | awk -v OFS='\t' '{print NR,$2,$4,$6}' # TIME TEST WITH DEINTERLEAVE ( echo ""Testing SeqFu deinterleave:"" echo -e ""TEST\tREAL\tUSER\tSYS"" for i in {1..11} do time seqfu deinterleave -o deinterleaved interleaved.fq done 2>&1 | paste - - - - | awk -v OFS='\t' '{print NR,$2,$4,$6}' echo ""Testing BASH deinterleave:"" echo -e ""TEST\tREAL\tUSER\tSYS"" for i in {1..11} do time paste - - - - - - - - < interleaved.fq | tee >(cut -f 1-4 | tr '\t' '\n' > deinterleaved.R1.fq) | cut -f 5-8 | tr '\t' '\n' > deinterleaved.R2.fq done 2>&1 | paste - - - - | awk -v OFS='\t' '{print NR,$2,$4,$6}' ) > deinterleave.time.txt ############ # CLEAN UP # ############ rm -f R[12].fq interleaved.fq de_R[12].fq ```","Markdown" "Bioengineering","telatin/seqfu2","bench/deinterleave.md",".md","383","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | |:---|---:|---:|---:|---:| | `seqfu deinterleave -o deinterleaved. interleaved.fq` | 4.194 ± 0.060 | 4.086 | 4.311 | 1.00 | | `paste - - - - - - - - < interleaved.fq \| tee >(cut -f 1-4 \| tr '\t' '\n' > R1.deinterleaved.fq) \| cut -f 5-8 \| tr '\t' '\n' > R2.deinterleaved.fq` | 5.106 ± 0.057 | 5.007 | 5.196 | 1.22 ± 0.02 | ","Markdown"