[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-09
Objective: read a bounded strand interval from the named synthetic contig.
Pinned inputs: {"chromosome":"px_core_A","start":1107,"end":1133,"strand":"+"}.
Do not substitute values from another genome or external service.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Select a specific sequence region by genomic coordinates (start-end position), highlighting it in the genome view. This sets the region as the active sequence selection, useful for subsequent operations like copy, extract, or analysis.

Open the benchmark interface and automatically start a benchmark run with the specified configuration. Supports selecting test suites, timeouts, and report options.

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.

Create BLAST protein database from loaded genome using 6-frame translation

Create BLAST nucleotide database from a specific chromosome of the currently loaded genome. Use this ONLY when you want to index a single chromosome and have its exact name from the loaded genome (e.g. U00096, NC_000913.3). Do not use this for the entire genome.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In read-only fixture PX-32, look up the exact synthetic gene identifier fxg12 without moving the genome view.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Restore a saved genome browser view state by ID or name, including chromosome position, visible tracks, track settings, and active tab when available.

Select a specific gene by name or locus tag, highlighting it in the genome view and showing its details. This sets the gene as the active selection, making it the target for subsequent operations like copy, edit, analyze, etc.

Save the current genome browser view state including chromosome, position, visible tracks, track settings, and active tab. Use this for workspace/layout snapshots that can be restored later by name; use bookmark_position for simple coordinate region bookmarks.

Jump directly to a gene location by gene name or locus tag. This is the PRIMARY tool for navigating to genes when you know the gene name.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In read-only fixture PX-33, look up the exact synthetic gene identifier fxg13 without moving the genome view.

Open and view a markdown (.md) file in a dedicated viewer window with syntax highlighting. The viewer renders markdown content with proper formatting, code highlighting, and a dark theme.

Export sequences from the current genome view in FASTA format

all genes cds intergenic features_only background_only

gene CDS tRNA rRNA misc_feature regulatory

Zoom the genome browser view to fit a specific gene, centering on it with configurable padding. This changes the visible region to show the entire gene with surrounding context. Use this when the user asks to zoom to a gene, focus on a gene, center view on a gene, or fit a gene in view. NOT the same as select_gene which only highlights without zooming.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In read-only fixture PX-36, look up the exact synthetic gene identifier fxg16 without moving the genome view.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In read-only fixture PX-37, look up the exact synthetic gene identifier fxg17 without moving the genome view.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In read-only fixture PX-38, look up the exact synthetic gene identifier fxg18 without moving the genome view.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In read-only fixture PX-39, look up the exact synthetic gene identifier fxg19 without moving the genome view.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-40
Objective: resolve an exact synthetic locus without changing the visible region.
Pinned inputs: {"name":"fxg20","navigate_to_gene":false}.
Do not substitute values from another genome or external service.

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.

Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to "show", "display", or "view" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Audit fixture PX-63: list CDS records on px_core_A between 1470 and 1565, capped at 7.

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.

List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.

Get list of all currently loaded files in the genome browser with their complete paths and metadata

Export coding sequences (CDS) in FASTA format

List current tasks in the workspace task tracking system, optionally filtered by status.

all pending in_progress completed failed

List all available tools in the system, organized by category. Use this to discover what functionality is available or to get help with available commands.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Audit fixture PX-64: list CDS records on px_core_B between 1607 and 1705, capped at 7.

List all available plugins in the system, including installed, enabled, and marketplace plugins. Provides comprehensive plugin information and status.

all installed enabled disabled available outdated

name version status last_used popularity

Display the Action List Manager interface for queued sequence-editing Actions. Actions are genome edit operations, not checklist Tasks.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Audit fixture PX-65: list CDS records on px_core_A between 2570 and 2671, capped at 7.

Get the current sequence-editing Action queue. Actions are queued genome edit operations, not checklist Tasks.

Get the list of all chromosomes (contigs/scaffolds) in the currently loaded genome, including their names, lengths, and which one is currently selected. Use this when the user asks about chromosome names, genome contigs, scaffold list, or wants to know what chromosomes are available.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Audit fixture PX-66: list tRNA records on px_core_B between 2707 and 2796, capped at 7.

Get predicted operon structures for a chromosome from loaded annotations. Returns operon coordinates, strand, gene count, member genes, and length. Use this when the user asks to show, list, find, predict, or inspect operons in the current genome.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Audit fixture PX-67: list CDS records on px_core_A between 3670 and 3762, capped at 7.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Audit fixture PX-69: list CDS records on px_core_A between 4770 and 4868, capped at 7.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Audit fixture PX-70: list CDS records on px_core_B between 4907 and 5008, capped at 7.

Rank gene-associated annotation features for curation using deterministic quality signals. Covers CDS, gene, mRNA, coding and non-coding RNA types, collapses co-located duplicate records, and prefers CDS at a shared locus.

include exclude-active exclude-completed exclude-covered


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-71
Objective: filter pinned feature records inside a coordinate window.
Pinned inputs: {"chromosome":"px_core_A","start":5870,"end":5959,"type":"tRNA","limit":7}.
Do not substitute values from another genome or external service.

Filter BLAST search results by identity, E-value, coverage, or hit count. Defaults to the most recent BLAST search, so the filter criteria are usually the only arguments needed.

Open the benchmark interface and automatically start a benchmark run with the specified configuration. Supports selecting test suites, timeouts, and report options.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the complete pinned annotation px014 from undefined for synthetic audit PX-94.

Load annotation files (GFF/BED/GTF) directly with file path specification or via file dialog

Update the status, title, or progress of an existing task in the tasks list.

Delete a genome annotation by identifier (locus_tag, gene name, or protein_id) with change tracking. Use this when the user explicitly asks to delete or remove a specific annotation. NOT the same as delete_sequence which removes sequence data.

Get protein annotations from UniProt

Create a new user-defined annotation

gene CDS mRNA tRNA rRNA promoter regulatory terminator ribosome_binding_site primer other


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the complete pinned annotation px015 from undefined for synthetic audit PX-95.

Cancel an annotation research workflow while retaining a durable task audit record.

Get protein annotations from UniProt

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the complete pinned annotation px016 from undefined for synthetic audit PX-96.

Get protein annotations from UniProt

Get the per-genome revisioned annotation ChangeSet audit trail.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the complete pinned annotation px017 from undefined for synthetic audit PX-97.

Create a new user-defined annotation

Get protein annotations from UniProt


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the complete pinned annotation px018 from undefined for synthetic audit PX-98.

Create a new user-defined annotation


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the complete pinned annotation px020 from undefined for synthetic audit PX-100.

Assess one resolved gene annotation feature with a deterministic completeness and curation-quality policy. Returns a 0-100 quality score, concrete reasons, missing fields, and recommended research focus. Co-located gene/CDS duplicates resolve to CDS.

Create a new user-defined annotation


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve the complete pinned annotation px001 from undefined for synthetic audit PX-101.

Create a new user-defined annotation


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-102
Objective: load the complete record for one pinned locus identifier.
Pinned inputs: {"identifier":"px002","full_details":true}.
Do not substitute values from another genome or external service.

Load genome files (FASTA/GenBank) directly with file path specification or via file dialog

Load sequencing reads files (SAM/BAM) directly with file path specification or via file dialog

Load WIG track files (single or multiple) directly with file path specification or via file dialog

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px005 on px_core_A in audit PX-125.

Download and cache the current AlphaFold protein structure selected from official prediction metadata by UniProt ID or gene name. PDB confidence values are returned per residue and remain embedded in the PDB B-factor column.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Show, hide, or toggle an individual panel in the genome browser Sidebar.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Download protein 3D structure from PDB database by PDB ID or gene name. Retrieves experimental structures with resolution data.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px006 on px_core_B in audit PX-126.

Select a specific gene by name or locus tag, highlighting it in the genome view and showing its details. This sets the gene as the active selection, making it the target for subsequent operations like copy, edit, analyze, etc.

Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px007 on px_core_A in audit PX-127.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px008 on px_core_B in audit PX-128.

Retrieve detailed information for a specific InterPro entry including description, member databases, protein matches, and structural data.

Zoom the genome browser view to fit a specific gene, centering on it with configurable padding. This changes the visible region to show the entire gene with surrounding context. Use this when the user asks to zoom to a gene, focus on a gene, center view on a gene, or fit a gene in view. NOT the same as select_gene which only highlights without zooming.

Zoom in the current view by a specified factor to see more detail of the genomic region


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px009 on px_core_A in audit PX-129.

Jump directly to a gene location by gene name or locus tag. This is the PRIMARY tool for navigating to genes when you know the gene name.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px010 on px_core_B in audit PX-130.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px011 on px_core_A in audit PX-131.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Fetch read-only gene details for synthetic locus px012 on px_core_B in audit PX-132.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-133
Objective: inspect the read-only details of one synthetic gene.
Pinned inputs: {"geneName":"px013","chromosome":"px_core_A"}.
Do not substitute values from another genome or external service.

Get the list of all chromosomes (contigs/scaffolds) in the currently loaded genome, including their names, lengths, and which one is currently selected. Use this when the user asks about chromosome names, genome contigs, scaffold list, or wants to know what chromosomes are available.

Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-164
Objective: collect typed features around a specified center coordinate.
Pinned inputs: {"chromosome":"px_core_B","position":1641,"distance":1321,"featureTypes":["CDS"]}.
Do not substitute values from another genome or external service.

Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position, genes around a location, or what is nearby a genomic coordinate. NOT the same as navigate_to_position which moves the view, or list_annotations which lists all annotations in a region.

Calculate GC content for a chromosome coordinate range from the currently loaded genome. Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.

Load genome files (FASTA/GenBank) directly with file path specification or via file dialog

Search for genomic features by ANNOTATION TEXT, FUNCTION KEYWORD, or FEATURE TYPE (e.g., find all tRNA, all kinase-related CDS, all transport proteins). This is a BROAD search across all feature types. Do NOT use this to look up a specific gene by its name — use find_gene_by_name or jump_to_gene instead.

Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to "show", "display", or "view" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-195
Objective: derive the opposite-strand representation of the supplied oligo.
Pinned inputs: {"sequence":"CGTTAGACTAGGAGGTAAAAACCGTATTG"}.
Do not substitute values from another genome or external service.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).

Run BLAST on a sequence extracted directly from a loaded genome chromosome region.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-226
Objective: decode a coding fragment with the declared code-table options.
Pinned inputs: {"dna":"ATGCAATATAAACTGACCTAA","reading_frame":1,"genetic_code":"bacterial","include_stop_codons":false}.
Do not substitute values from another genome or external service.

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

standard vertebrate_mitochondrial bacterial archaeal

Stop the currently running benchmark. Gracefully terminates the benchmark execution and saves any partial results collected so far.

Quickly create BLAST databases (both nucleotide and protein) for the entire currently loaded genome. Use this as the default/quick way to index the genome when no specific chromosome name is specified. Automatically associates databases with the genome for smart database selection.

Create BLAST protein database from loaded genome using 6-frame translation


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-257
Objective: measure the G/C fraction of the explicit nucleotide sample.
Pinned inputs: {"sequence":"AGCGGGTAAGTGCCGACACAGCACAGCC","normalize_case":true}.
Do not substitute values from another genome or external service.

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.

Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-288
Objective: measure symbol-level Shannon complexity for the explicit sample.
Pinned inputs: {"sequence":"GAGGTTTCACGATAGAAGTGATGAGGTTTGGG"}.
Do not substitute values from another genome or external service.

Load sequencing reads files (SAM/BAM) directly with file path specification or via file dialog

Load genome files (FASTA/GenBank) directly with file path specification or via file dialog


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-319
Objective: derive molecular mass for the declared polymer type.
Pinned inputs: {"sequence":"GCGCCGCCGATTGCGCTTCATGTTCTA","type":"dna"}.
Do not substitute values from another genome or external service.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Run BLAST on a sequence extracted directly from a loaded genome chromosome region.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-350
Objective: inspect length, composition, melting behavior, and hairpin risk of the oligo.
Pinned inputs: {"sequence":"AGAAAAGCTCAGTGAGCTGTGA"}.
Do not substitute values from another genome or external service.

Calculate biochemical properties like melting temperature (Tm), GC content, and length for a given DNA primer sequence (18-35 bp). Use this to check if a sequence is suitable as a PCR or sequencing primer.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-381
Objective: scan the explicit template for exact matches to the supplied primer.
Pinned inputs: {"sequence":"GCACCGAGTGGTAGTCCC","templateSequence":"CGATGGGGGACAACGTAACCCAGTGTAATGTATGAGCCGAGTAGGCCCAAGGGATTCGGTGCGTGCTATTGCCAGTATACGCAGGCGACCGTCCCTTCGTAACCAAGTACGTGATAACCGCTCGATGGTATGGCTACACTGGGATATCGAATGGTGGAGATGAAGTGTCCATGCTCGTAGTAGTAGGCAACAGGTTCATTAACGCGCTCCCCACCCCAAGCATAACGAAATTTCAAGCGGATTTGCTGAAACCGATTTATCGGCAAGTATTGCATTGAGGCTGTAACTGCGCGGCTTTAATTAGTAGAATGAGGCGTGCGGGGGGTAATTAGCGTACACTTTGTAAGAATTGTGCCGTATGCCTCCTTGAATGTAATGTCAACATTATTGGGCACCGAGTGGTAGTCCCTTGCGTAGCCTAAGG","maxMismatches":0,"max3PrimeMismatches":0}.
Do not substitute values from another genome or external service.

Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Save a primer oligo to the primer library (stored separately from the genome, never written into the genome file). Binding sites are predicted automatically; provide chromosome/start/end only to pin a specific manual placement.

Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate BamHI sites in the explicit pinned DNA for digest check PX-404: CTCATTCGGTGCCGAACCTTTCCTGGGGAATTTTATATGATACATACCGCCCTGACCGAGTGTGGAGGCGCATCGTTGCATACGCAGAATTCTGCCGAATCACCCAAGCGCGGCAATATTCCTTCAATCTCCACAAATATGGATAGCGCTCGAGATTTCTACCCATCTTTTTAAATGAACACGCCGTTTAAAGCCCCAATCTCGTTCTCAATCTTACGCCTCGCTGAATCTCTCCCCAGAAAAAGCAGACTCAGCGGGCATTTTAATCCTCCATGTGACTTTAGGGAAGCCGTAAAAGCTGGGTTGGTATCCAACAGCGCTTGTATAATAGGCCAGTAACCAACTTAAGAATATCCTAACCGCCGGCGAAGCCTACTCGTCAAGTTATACAAATCATCGCTTGACTGTGATTGGGCGGGAGGATCCGTCATGTCTGCCTCAGCCAA.

Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.

Validate a local BLAST database integrity and format

Get the current content of the sequence clipboard. The clipboard holds sequences that have been copied or cut from the genome using copy_sequence or cut_sequence. Use this to check what sequence is currently stored in the clipboard before pasting or to verify a copy/cut operation. NOT the same as get_action_list which lists pending editing actions.

Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.

Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate HindIII sites in the explicit pinned DNA for digest check PX-405: GGTGTTGACTTCGCAGCTGCGCGAAAGTACCTGCATAGGGCCGTAGCCTCATTGCTTGCTCATGTTACGCTCATGGAAGTAAAAGACGCCAAATGAGCGAGATATGGGAACGTACATTACGGTGTAGGCCCCCTACAGTTATGTGTACTCCCTACCCTAACTAGGGCTGCGAGGAGCCTGCAGATACTCACGGGTTGAGAGCTACTTTCGAAGTGGGCTCCGAGTAAGGAAAACCTGTCCGCTGTTTAGGGGGTTCATATATGGCCCCTCAGTAACATCAAGGCATTAGTCGGTTGCTCTAGTGTTGGTGTACGACATCCGGGCATTTGGGACGAGCCTCCTTCAGGTCACGCTCCTCAACCGCGGAGATATTAGCGTTAGTAAACGTCAGCACAAGAGGCTACCTCCCTAGCGACTTCCCAAGCTTGCGTCTCAAAATAATAGTAGA.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Detect whether a sequence is DNA, RNA, or protein


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate XhoI sites in the explicit pinned DNA for digest check PX-406: CTGGCTAAAACCTGGCGAGCGACATCCTTAGACCAAGGTCAGATATTTTGGGATGACTTGTAACCGCCGTATTCTGAGGCACCTACGTAGTAGGTCGTACGGATACTATCTTGTAATAGAAGTAAGGGTCAACACGGGTGGATAGTGCTTCCAGTCCCCCTTGGACGATCGTGGACCCCCTCTCCGGTATCAGAAATATCTGTGGGTGTCCCAGAGAATGTCACCAATTCGCTACGACCAGGCTTACCTTGCCAATAGACCGCACTTCCGGCGCCATTATGAATAGCGTTCGCCTATACAAAATCTAGCTCGCAACAGCGGAGGTTATAGCTAAAGAGTAGTACGCGTGGATACTACGCACTAGTGTCCGCGCCTAGTATAAGAACCGTATAAACACTTTTACAGGCAGGCCGTGTGACGTCCTCGAGTAGGTTCGCAACTAGTCAGCTA.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate PstI sites in the explicit pinned DNA for digest check PX-407: GTAATATTATTCTCACAGAGCCTAAGTAAAGTGCTTACTAGACGCCGAACGCGACTCCCATTCCTGTCGGCCCGGACTCGAATTTACAAGTGAGTGCTCGTGTAGCGCGCGCTTCCCCCCTCGCTCAACTTCAACGCCAGACTTTGGCCCGTAATCGACGGTCGCGAGGAGAACTCTACCGCATCATTGTAAAAATTGTGACATGTGGTGATCCGATTTGAATTAGGTACAGTCCTCAGGCGCTTATGAAGGGCCCGCTGAGGAGGTGTTACGTTTTACCAAAGTACCATCAAGCCTAGTCTCTTGCTTAGCTCATAAAGGGTGAATGCCTCTTGCGGTGAAAGAGCGCATAACGAACTAGAGCGAGGTATCAATTGACAAACAAAAGAGCGACATGTTTGTTCGGGCGCGATGTAGTTCGCGCTGCAGGTAAGCTCCCGCGGCCTCAAACA.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate NotI sites in the explicit pinned DNA for digest check PX-408: GAATCACTTTCTCTATCTCGCGTGGGATACTCTGCCCCGTATTGGATAGGCCGCCGGCCCCCCCCACTTGGGCTCCACAAATGCTGACATGCCTGGTCCCAAGCTACGCTACATATTGTTATAGGGGACAGATTATGACGCCCTACACATGGCCCAGAATGAATAGGCCCGAGATCTCCATATCCGAACAATTAAGGCCTGTCATTCTGTGGGCGAGGGGCAGGTCGGAGCTCAGACGCCCCTTAGCCATGCGCACGGGTTGGCGTGTGCCGCATGTGCCATTTAAGTTGCACCTAGCAGTCCATTTTCGCGGCCGATCACGACCTATCGCGTCTTAGAATCACAGTAATACGTTGCTATATCTTCACGGGAGAGTGCTCCCGCGAGTCATTCTTTAACCGACACTGTCCGCTAAGCGATATATGCGGCCGCTGTGAGGCTACCTTCTCCGAACCC.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate EcoRI sites in the explicit pinned DNA for digest check PX-409: ACATATAGGAGGCTCTATTAATGATGTTCCCAAAAGCATTACCACGTTCACGAGATTACAGGGTGAGATGGATTAAAAGTTGGTTGGCGGCCTAGGATTGACACAGATTCGTTTTAGGTCACCCACTACGGCTAGCCCGATCAAAGCCTATAATGTTGAACAATGCATGCTGGCGGACTAGTCTCCGGGCCGGTGTAAGCAGCTCTTTGGTATACTGATGCATCTTTATAGAATATGCCCTCCCGTTTTGATCATGCGGGAGAGAAAAAGCTTAGTTCTCAGTGTGCCTCTCAGCTTCCACATGGCAAGGGAGCTGCGGGTATGTACTAAACCTAATCACACTCACGAAGCTGATAGTCTCCAAAGTTGAAGACAAGGACCGATAGTTTCCGAACCGAGGCCACTGGGATTGATGAGGAGTCTATGAATTCCGCATTTGTCTCATTGGCA.

Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate BamHI sites in the explicit pinned DNA for digest check PX-410: GTCTTTAGACACCCCGTGCTGCCCCTATTGGTCTCCATCGGAGAGAGGTGCGAATTCCTAAGTTGAGTGCGGCCCTGTCGAAGTTTTTAGATGAGGTCGTCGTGAGTCGGGGTGCAGAGGTACAATCCTATGTCTCGGGCGGATTTGCACCGAAGTCTTCTTACCTTGCCAAGGTCGGTTGGCTTGGATAGCTTCGAAGTGGGCAACGCTCGGTTGCGTCAAAGCTAACCGACGCGTTTACGAGTACAATCAAATGTGCCGCAAGTACATACGCGGTCCACGTCGTTCGGATAGCGGCTTGACGAAGGTGGATCTAACTATTCCGGAAGGGATAAGCGAGGCTTGGCGAATAGGACCGAAGGGGAGGCTCTCTGCGAGAGTATCATTTTGAGACGAGGAGGATCGGTAACAGGCACCGCGCTCGCTGGATCCATTTCCTTTGTCAGAGGGTA.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Locate HindIII sites in the explicit pinned DNA for digest check PX-411: ATTACAGAACCAATAAATGTTGATTGAGTCAAAGTACATCCGACAGTCAACTTAAAGCGGAGATAGAGGATAAACGCGATGTTCGTCTAATTACTAAACAAGGATTTAGTGAGGTCGGGATTTTACACCTACCTTGTTGGAGAGTTTGCAATACGCCTGGGGATCCCGGTATCGCACTTTCGTACAATTCCTCACCACTCGAGCATTCGAAGGTTCTCCGAGTAGTGCCTCGTATGAATCGCTTAAGCTCGATCTATATTTTACTCAAGTAGTCTCTGTCTATTCCCAGGTCAACTTAATGTGTCAACTCCGTCACCCCAACGGAAGTACGTGCTAGTTCGTCTCGGGCTACCGATGCACACTCCCCTCGTTTATACAAAACTCTAAATATGCTCATTATGCGTCAAACCTTCTCATCGGCAGGTTGAAGCTTGCTCGAGGGGCCCAATATAAT.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-412
Objective: scan explicit DNA for recognition sites of the declared enzyme.
Pinned inputs: {"enzyme":"XhoI","sequence":"AGCCCGCATCTCTTTACTCTGTGTTCCCATAATTCTTGTGGCATCGTCTGACAGATATAGCCACGATCCTAGTTGCGTGGTATTTTGAAGCCGTTCCTTAAAGGATCTGTGCTAATAACCAGTCTAACCTGCGCCGTTGTAGCGGGCGTACGAATCCCAGCCGCAGCCCTATTGTAGGGCACCTGACTCGTCAGGCAAGACTTTCGACGTGACACCGCAAACCTCGAGCCGATAATTCTTCTCTCCTCCCTTGCGTTGGAGCTCGCAATTAAAGGTGAGCATTTGTCTTAACCGCCCTCCCGCGATTGTGGGACATGTAAGGTCCCAGCTCATGATGCATGCCTTTCGGCAACTTAAGCAACTCACGGGGACTCAATAGAACACTAGGACGCAAACTCATTGTCGTGGACGTTTGTGCAATCTTAAGCCTCGAGTGTTTACTGCATGTTAGGGGTT"}.
Do not substitute values from another genome or external service.

Load genome files (FASTA/GenBank) directly with file path specification or via file dialog


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-443
Objective: compute fragment boundaries after the declared enzyme combination.
Pinned inputs: {"enzymes":["PstI","EcoRI"],"sequence":"ATTGCTGACCTGATGTGTTCTAGTCGAGTGTGTTATCGTGCCGTGCAGCTAGCGCGGAAATTAGGGGACCGACCCGGTACCAAGGTGATGCCAGGATGTATGGCACGGAATTTTGTTCCCAGTAGGCGATGGACACGAGCCTGAAATGCAAGCGACGTCGAGATGGGGCCCGCGTTACTTATGGTAGGAGCTTTAAGTGTCAGGCTTGAGCTATGTTCCCGTTGATTGTAACCTAACTGTACGTGTATATCAGCGTAATATGTTAATATACCGACCCGCTGGCATATGGTTAGGGAATTTCGCTCTCACGCTTGACCGCCATTGTTCTTCTACCGACCCACGGTAGTAATTGTGCCCTGCCTCGGTCAGATGAGCTATTCCGGAGCACATCCTTATCCTATCGGACAAACCAGAGGTAAATAAAAATGTAAAACCGACCCTCGTTAGTATACCATTTCACTGCAGGCTACTATATTCTACGAATTCGACTTAAGGCTAGGTACTCACAC"}.
Do not substitute values from another genome or external service.

Performs an in-silico restriction digest of a chromosome or sequence using one or more restriction enzymes. Calculates fragment positions, sizes, end types (5' overhang, 3' overhang, blunt), and provides digest map for gel electrophoresis visualization.

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.

Run BLAST on a sequence extracted directly from a loaded genome chromosome region.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for the synthetic protein record pcf017 in Synthetic bacterium Beta, limiting the audit PX-497 to 4 entries. This is a UniProt lookup, not a genome-gene search.

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.

experimental homology predicted uncertain

Get detailed protein information from UniProt

Search PDB database for experimental protein structures by gene name. Returns available X-ray crystallography, NMR, cryo-EM, and other experimental structure data.

x-ray
nmr
cryo-em
neutron
fiber diffraction

Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for the synthetic protein record pcf019 in Synthetic bacterium Alpha, limiting the audit PX-499 to 4 entries. This is a UniProt lookup, not a genome-gene search.

Search AlphaFold database for protein structures by gene name. Returns predicted 3D structures with confidence scores and metadata.

Advanced UniProt search with multiple query fields, filters, and complex search criteria. Supports boolean operators and field-specific searches.

Search UniProt database for protein information


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for the synthetic protein record pcf001 in Synthetic bacterium Alpha, limiting the audit PX-501 to 4 entries. This is a UniProt lookup, not a genome-gene search.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Search for genomic features by ANNOTATION TEXT, FUNCTION KEYWORD, or FEATURE TYPE (e.g., find all tRNA, all kinase-related CDS, all transport proteins). This is a BROAD search across all feature types. Do NOT use this to look up a specific gene by its name — use find_gene_by_name or jump_to_gene instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for the synthetic protein record pcf002 in Synthetic bacterium Beta, limiting the audit PX-502 to 4 entries. This is a UniProt lookup, not a genome-gene search.

Create BLAST protein database from loaded genome using 6-frame translation

Get protein annotations from UniProt


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search the pinned UniProt protein snapshot for the synthetic protein record pcf003 in Synthetic archaeon Gamma, limiting the audit PX-503 to 4 entries. This is a UniProt lookup, not a genome-gene search.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-505
Objective: query the frozen protein snapshot with the supplied identity filters.
Pinned inputs: {"search_query":"pcf005","organism":"Synthetic bacterium Beta","max_results":4}.
Do not substitute values from another genome or external service.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX008A with its sequence for synthetic audit PX-528.

Retrieve detailed information for a specific UniProt entry including sequence, annotations, functions, and cross-references.

Detect whether a sequence is DNA, RNA, or protein

Perform BLAST search on a protein sequence

Search InterPro database for domain families, functional sites, and protein signatures using keywords, names, or descriptions. Enhanced with advanced filtering and batch processing capabilities.

name description keyword signature go_term literature all

Pfam SMART PROSITE PRINTS PANTHER Gene3D SUPERFAMILY PIRSF HAMAP CDD NCBIfam SFLD

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Retrieve detailed information for a specific InterPro entry including description, member databases, protein matches, and structural data.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX009A with its sequence for synthetic audit PX-529.

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Open an interactive 3D protein structure viewer from cached data, a local PDB file, an online PDB URL, a UniProt/AlphaFold accession, a PDB ID, or a gene name. Online structures are downloaded automatically.

chain secondary atom residue temperature


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX010A with its sequence for synthetic audit PX-530.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX011A with its sequence for synthetic audit PX-531.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX012A with its sequence for synthetic audit PX-532.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX013A with its sequence for synthetic audit PX-533.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX014A with its sequence for synthetic audit PX-534.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Retrieve pinned protein entry QX015A with its sequence for synthetic audit PX-535.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Validation card PX-536
Objective: load one frozen protein record and include its amino-acid sequence.
Pinned inputs: {"uniprot_id":"QX016A","include_sequence":true}.
Do not substitute values from another genome or external service.

Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

Get detailed protein information from UniProt

Get protein annotations from UniProt


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card GW-px006
Resolve fxg06 in the frozen genome without moving the view. Feed the returned contig and bounds into a sequence read, then feed that read result into frame-one translation.

Stop the currently running benchmark. Gracefully terminates the benchmark execution and saves any partial results collected so far.

Get the list of all chromosomes (contigs/scaffolds) in the currently loaded genome, including their names, lengths, and which one is currently selected. Use this when the user asks about chromosome names, genome contigs, scaffold list, or wants to know what chromosomes are available.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card GW-px006
Resolve fxg06 in the frozen genome without moving the view. Feed the returned contig and bounds into a sequence read, then feed that read result into frame-one translation.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card GW-px006
Resolve fxg06 in the frozen genome without moving the view. Feed the returned contig and bounds into a sequence read, then feed that read result into frame-one translation.

[Tool] {"success":true,"sequence":"ATGGGTCAATATAAATAA","length":18,"chromosome":"px_core_B","start":2738,"end":2755,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card AW-ann-px-012
Filter the frozen CDS records around 6038-6058 on px_core_B. Use the first returned locus tag, rather than a guessed identifier, for a full-detail lookup.

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Add a persistent visual highlight (a colored box) over a genomic region, spanning the full height of the ruler and tracks. Unlike select_sequence_region (which sets a single active selection for copy/extract), this supports MULTIPLE and OVERLAPPING highlights that stay visible while panning and zooming. Use when the user asks to "highlight", "mark", or "box" a region so it stands out. Each call adds one more highlight; use clear_highlights to remove them all or remove_highlight to remove one.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.

Export protein sequences translated from CDS in FASTA format

Assess one resolved gene annotation feature with a deterministic completeness and curation-quality policy. Returns a 0-100 quality score, concrete reasons, missing fields, and recommended research focus. Co-located gene/CDS duplicates resolve to CDS.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card AW-ann-px-012
Filter the frozen CDS records around 6038-6058 on px_core_B. Use the first returned locus tag, rather than a guessed identifier, for a full-detail lookup.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card PW-QX008A
Query the frozen UniProt protein snapshot for Synthetic bacterium Beta record pcf008. Resolve the first accession to a sequence-bearing entry, then use that returned amino-acid sequence for a protein-mass calculation. This is a UniProt lookup, not a genome-gene search.

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.

Retrieve detailed information for a specific UniProt entry including sequence, annotations, functions, and cross-references.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.

Search AlphaFold database for protein structures

Advanced UniProt search with multiple query fields, filters, and complex search criteria. Supports boolean operators and field-specific searches.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card PW-QX008A
Query the frozen UniProt protein snapshot for Synthetic bacterium Beta record pcf008. Resolve the first accession to a sequence-bearing entry, then use that returned amino-acid sequence for a protein-mass calculation. This is a UniProt lookup, not a genome-gene search.

[Tool] {"success":true,"results_count":1,"entries":[{"accession":"QX008A","protein_name":"Pinned catalytic family 008","gene_name":"pcf008","organism":"Synthetic bacterium Beta","reviewed":true,"length":29}]}

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User]
Dependency card PW-QX008A
Query the frozen UniProt protein snapshot for Synthetic bacterium Beta record pcf008. Resolve the first accession to a sequence-bearing entry, then use that returned amino-acid sequence for a protein-mass calculation. This is a UniProt lookup, not a genome-gene search.

[Tool] {"success":true,"results_count":1,"entries":[{"accession":"QX008A","protein_name":"Pinned catalytic family 008","gene_name":"pcf008","organism":"Synthetic bacterium Beta","reviewed":true,"length":29}]}

[Tool] {"success":true,"entry_info":{"accession":"QX008A","protein_name":"Pinned catalytic family 008","gene_name":"pcf008","organism":"Synthetic bacterium Beta","reviewed":true},"protein_sequence":"MIKLMNPQRSTVWYGAVLIPFYWSTCMNQ","sequence_length":29}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] BLAST this DNA sequence against the nucleotide database

Perform BLAST sequence similarity search against various databases. Supports nucleotide and protein sequences with comprehensive search options.

Validate a local BLAST database integrity and format

Perform BLAST search on a DNA sequence

Run BLAST on a sequence extracted directly from a loaded genome chromosome region.

Delete a local BLAST database

Perform BLAST sequence similarity search using NCBI online databases


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Search for similar proteins to this sequence

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Perform BLAST search on a protein sequence

Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.

Search for genomic features by ANNOTATION TEXT, FUNCTION KEYWORD, or FEATURE TYPE (e.g., find all tRNA, all kinase-related CDS, all transport proteins). This is a BROAD search across all feature types. Do NOT use this to look up a specific gene by its name — use find_gene_by_name or jump_to_gene instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Find homologous genes in E. coli only

Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.

Find genes associated with a specific metabolic pathway

Get predicted operon structures for a chromosome from loaded annotations. Returns operon coordinates, strand, gene count, member genes, and length. Use this when the user asks to show, list, find, predict, or inspect operons in the current genome.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Return a screenshot directly through MCP without saving a file

Capture a PNG or JPEG screenshot of the full CodeXomics application interface or rendered genome tracks

Open a local image file in the system image viewer

Download a file from the internet (URL) to a local path. Useful for downloading reports, data files, images, or any other files accessible via HTTP/HTTPS URLs.

Load genome files (FASTA/GenBank) directly with file path specification or via file dialog

Load variant files (VCF) directly with file path specification or via file dialog

Load operon definition files (JSON/CSV/TSV/TXT) directly with file path specification or via file dialog. Supports RegulonDB TSV format.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，精确查找基因 fxg02（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.

Retrieve detailed information for a specific InterPro entry including description, member databases, protein matches, and structural data.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，精确查找基因 fxg02（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，精确查找基因 fxg02（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-536 - 链的序列，并计算该序列的熵。

Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.

Retrieve a resumable DGR research workflow; annotation:propose callers materialize completed proposals as reviewable ChangeSets, while research-only callers can defer that step.

Retrieve change history for a specific annotation or the entire genome

Get the current content of the sequence clipboard. The clipboard holds sequences that have been copied or cut from the genome using copy_sequence or cut_sequence. Use this to check what sequence is currently stored in the clipboard before pasting or to verify a copy/cut operation. NOT the same as get_action_list which lists pending editing actions.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-536 - 链的序列，并计算该序列的熵。

[Tool] {"success":true,"sequence":"AACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":37,"chromosome":"px_core_B","start":500,"end":536,"strand":"-","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并按阅读框 3 翻译成氨基酸。

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Get detailed information about a specific DNA marker/ladder, including all band sizes, recommended gel percentage, and description.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并按阅读框 3 翻译成氨基酸。

[Tool] {"success":true,"sequence":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"strand":"-","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

Remove all tasks from the workspace task tracking system.

Add a new task to the workspace tasks list for tracking progress during complex operations.

Update the status, title, or progress of an existing task in the tasks list.

Delete a task from the workspace tasks list.

List current tasks in the workspace task tracking system, optionally filtered by status.

Delete primers from the library. Requires confirm=true. Optionally scope to one chromosome to remove only pinned placements there.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}

[Tool] {"success":true,"updated":1,"task_id":"task_763"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 清空待办任务列表，新建标题为 PX-verify 的进行中任务（进度 25），将其标记为已完成（进度 100），删除该任务，最后列出全部任务确认。

[Tool] {"success":true,"cleared":1}

[Tool] {"success":true,"task_id":"task_763","id":"task_763","title":"PX-verify","status":"in_progress","progress":25}

[Tool] {"success":true,"updated":1,"task_id":"task_763"}

[Tool] {"success":true,"deleted":1,"task_id":"task_763"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In the loaded genome browser, list the visibility of all tracks first, then open the proteins track.

Get the current visibility status of all tracks in the genome browser. Returns which tracks (genes, sequence, gc, variants, reads, proteins) are currently visible and their descriptions. Use this when the user asks about track visibility, which tracks are shown/hidden, or current track status. NOT the same as get_all_track_settings which returns detailed configuration/settings for each track.

Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.

genes gc_content sequence variants reads proteins primers actions wigTracks blast

Get current settings for all track types in the genome browser

Get current settings for a specific track type in the genome browser (genes, primers, reads, sequence, gc, variants, actions, blast, wigTracks, sequenceLine). For multi-instance tracks, provide file_id to get instance-specific settings.

genes primers reads sequence gc variants actions blast wigTracks sequenceLine

Get the complete schema of available settings for all track types

Get status of a specific agent


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In the loaded genome browser, list the visibility of all tracks first, then open the proteins track.

Get status of a specific agent


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 先列出已加载浏览器中所有轨道的可见性，然后打开蛋白质轨道。

Get current status of a workflow execution


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 先列出已加载浏览器中所有轨道的可见性，然后打开蛋白质轨道。


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并计算该序列的 GC 含量。

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.

Get comprehensive information about the loaded genome including chromosomes, annotations, statistics, and metadata. Use this to understand the available genomic data.

Get the per-genome revisioned annotation ChangeSet audit trail.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并计算该序列的 GC 含量。

[Tool] {"success":true,"sequence":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"strand":"-","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-548, then translate that retrieved DNA in reading frame 3.

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Get detailed information about a specific DNA marker/ladder, including all band sizes, recommended gel percentage, and description.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-548, then translate that retrieved DNA in reading frame 3.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACACGAGTA","length":49,"chromosome":"px_core_A","start":500,"end":548,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, find gene fxg09 exactly (do not navigate the view), retrieve the sequence of exactly the returned interval, then compute the GC content of that sequence.

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.

Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, find gene fxg09 exactly (do not navigate the view), retrieve the sequence of exactly the returned interval, then compute the GC content of that sequence.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, find gene fxg09 exactly (do not navigate the view), retrieve the sequence of exactly the returned interval, then compute the GC content of that sequence.

[Tool] {"success":true,"sequence":"ATGAAACTGACCGACGCTGAATTCTAA","length":27,"chromosome":"px_core_A","start":4801,"end":4827,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 关闭基因组浏览器中的读段轨道，然后重新检查当前轨道可见性。

Get the current visibility status of all tracks in the genome browser. Returns which tracks (genes, sequence, gc, variants, reads, proteins) are currently visible and their descriptions. Use this when the user asks about track visibility, which tracks are shown/hidden, or current track status. NOT the same as get_all_track_settings which returns detailed configuration/settings for each track.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 关闭基因组浏览器中的读段轨道，然后重新检查当前轨道可见性。

[Tool] {"success":true,"track":"reads","visible":false}

Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.

Get current settings for all track types in the genome browser


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-548, then return the reverse complement of that retrieved sequence.

Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).

List saved genomic region bookmarks and saved view states, optionally filtered by chromosome.

Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position, genes around a location, or what is nearby a genomic coordinate. NOT the same as navigate_to_position which moves the view, or list_annotations which lists all annotations in a region.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-548, then return the reverse complement of that retrieved sequence.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACACGAGTA","length":49,"chromosome":"px_core_A","start":500,"end":548,"strand":"+","format":"raw"}

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-536 - 链的序列，并按阅读框 1 翻译成氨基酸。


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-536 - 链的序列，并按阅读框 1 翻译成氨基酸。

[Tool] {"success":true,"sequence":"AACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":37,"chromosome":"px_core_B","start":500,"end":536,"strand":"-","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-542, translate it in reading frame 2, then calculate the molecular weight of the resulting protein.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-542, translate it in reading frame 2, then calculate the molecular weight of the resulting protein.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACA","length":43,"chromosome":"px_core_A","start":500,"end":542,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-542, translate it in reading frame 2, then calculate the molecular weight of the resulting protein.

[Tool] {"success":true,"sequence":"ATATCGACCTCCAATGTTGACGCAGAATCCTGGCAAAGCTACA","length":43,"chromosome":"px_core_A","start":500,"end":542,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Close the reads track in the genome browser, then re-check the current track visibility.

Get current settings for a specific track type in the genome browser (genes, primers, reads, sequence, gc, variants, actions, blast, wigTracks, sequenceLine). For multi-instance tracks, provide file_id to get instance-specific settings.

Get the complete schema of available settings for all track types


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] Close the reads track in the genome browser, then re-check the current track visibility.

[Tool] {"success":true,"track":"reads","visible":false}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，列出 px_core_B 上的注释，并取出第一条注释的完整信息。

List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.

Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.

Get list of all currently loaded files in the genome browser with their complete paths and metadata

Get the per-genome revisioned annotation ChangeSet audit trail.

List the durable, per-genome Deep Gene Research history used to prevent repeated annotation research across agents and automation runs.

active completed completed_unarchived failed cancelled

Retrieve a resumable DGR research workflow; annotation:propose callers materialize completed proposals as reviewable ChangeSets, while research-only callers can defer that step.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，列出 px_core_B 上的注释，并取出第一条注释的完整信息。


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，精确查找基因 fxg16（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。

Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., "all kinase genes", "all tRNA"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.

Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.

Retrieve detailed information for a specific InterPro entry including description, member databases, protein matches, and structural data.

Retrieve an annotation ChangeSet and its validation, approval, or commit state.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，精确查找基因 fxg16（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，精确查找基因 fxg16（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并按阅读框 3 翻译成氨基酸。

Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.

Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.

Get detailed information about a specific DNA marker/ladder, including all band sizes, recommended gel percentage, and description.

Get the benchmark results history. Returns statistics from all previous benchmark runs, including success rates, test counts, durations, and the latest run details.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] 在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并按阅读框 3 翻译成氨基酸。

[Tool] {"success":true,"sequence":"CGGAATTCCATGAACTTGCGGCTTACGGCTTGTATCTTGCGTTAAGTCC","length":49,"chromosome":"px_core_B","start":500,"end":548,"strand":"-","format":"raw"}

Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD "sequence". For visualizing genomic regions, use navigate_to_position instead.

Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:392-428, then calculate the molecular weight of that retrieved sequence.

Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:392-428, then calculate the molecular weight of that retrieved sequence.

[Tool] {"success":true,"sequence":"TACGCGTTGATGGCTGAATTCCGTTAAAGGCATGATG","length":37,"chromosome":"px_core_A","start":392,"end":428,"strand":"+","format":"raw"}


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In the pinned UniProt fixture corpus, search for "pinned catalytic", then fetch the full entry of the first search result.

Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.

Retrieve detailed information for a specific UniProt entry including sequence, annotations, functions, and cross-references.

Search InterPro database for domain families, functional sites, and protein signatures using keywords, names, or descriptions. Enhanced with advanced filtering and batch processing capabilities.

Advanced UniProt search with multiple query fields, filters, and complex search criteria. Supports boolean operators and field-specific searches.

Get status of a specific agent


[System] Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it.

[User] In the pinned UniProt fixture corpus, search for "pinned catalytic", then fetch the full entry of the first search result.

[Tool] {"success":true,"results_count":5,"entries":[{"accession":"QX001A","protein_name":"Pinned catalytic family 001","gene_name":"pcf001","organism":"Synthetic bacterium Alpha","reviewed":true,"length":29}]}

Get status of a specific agent