core/data/seed_backbones.py

"""
Seed plasmid backbones for the assembly workflow.

Provides demo backbone data for common expression vectors.
Sequences are truncated/representative for demo purposes.
"""
from __future__ import annotations

from typing import List

from core.models.plasmid import PlasmidBackbone, PlasmidFeature


def get_seed_backbones() -> List[PlasmidBackbone]:
    """Return demo plasmid backbones."""
    backbones = []

    # pUC19 — classic high-copy cloning vector
    backbones.append(PlasmidBackbone(
        name="pUC19",
        description="High-copy number E. coli cloning vector (2,686 bp). Contains lacZ-alpha MCS, ampicillin resistance, and pMB1 origin.",
        sequence="TCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTC",
        features=[
            PlasmidFeature(label="AmpR", feature_type="resistance", start=1629, end=2489, strand="-", color="#EF4444"),
            PlasmidFeature(label="pMB1 ori", feature_type="ori", start=2489, end=2686, color="#3B82F6"),
            PlasmidFeature(label="lacZ-alpha", feature_type="other", start=217, end=580, color="#10B981"),
            PlasmidFeature(label="MCS", feature_type="cloning_site", start=396, end=452, color="#F59E0B"),
        ],
        cloning_sites=["EcoRI", "SacI", "KpnI", "BamHI", "XbaI", "SalI", "PstI", "SphI", "HindIII"],
        source="library",
    ))

    # pcDNA3.1 — mammalian expression vector
    backbones.append(PlasmidBackbone(
        name="pcDNA3.1(+)",
        description="Mammalian expression vector (5,428 bp). CMV promoter, BGH polyA, neomycin/G418 resistance, SV40 ori.",
        sequence="GACGGATCGGGAGATCTCCCGATCCCCTATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCCAGTATCTGCTCCCTGCTTGTGTGTTGGAGGTCGCTGAGTAGTGCGCGAGCAAAATTTAAGCTACAACAAGGCAAGGCTTGACCGACAATTGCATGAAGAATCTGCTTAGGGTTAGGCGTTTTGCGCTGCTTCGCGATGTACGGGCCAGATATACGCGTTGACATTGATTATTGACTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCATAGCCCATATATGGAGTTCCGCGTTACATAACTTACGGTAAATGGCCCGCCTGGCTGACCGCCCAACGACCCCCGCCCATTGACGTCAATAATGACGTATGTTCCCATAGTAACGCCAATAGGGACTTTCCATTGACGTCAATGGGTGGAGTATTTACGGTAAACTGCCCACTTGGCAGTACATCAAGTGTATCATATGCCAAGTACGCCCCCTATTGACGTCAATGACGGTAAATGGCCCGCCTGGCATTATGCCCAGTACATGACCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTATTAGTCATCGCTATTACCATGGTGATGCGGTTTTGGCAGTACATCAATGGGCGTGGATAGCGGTTTGACTCACGGGGATTTCCAAGTCTCCACCCCATTGACGTCAATGGGAGTTTGTTTTGGCACCAAAATCAACGGGACTTTCCAAAATGTCGTAACAACTCCGCCCCATTGACGCAAATGGGCGGTAGGCGTGTACGGTGGGAGGTCTATATAAGCAGAGCTGGTTTAGTGAACCGTCAGATC" + "A" * 200,
        features=[
            PlasmidFeature(label="CMV promoter", feature_type="promoter", start=1, end=590, color="#8B5CF6"),
            PlasmidFeature(label="MCS", feature_type="cloning_site", start=895, end=1010, color="#F59E0B"),
            PlasmidFeature(label="BGH polyA", feature_type="terminator", start=1010, end=1234, color="#EF4444"),
            PlasmidFeature(label="NeoR/KanR", feature_type="resistance", start=1850, end=2644, strand="+", color="#10B981"),
            PlasmidFeature(label="SV40 ori", feature_type="ori", start=1234, end=1450, color="#3B82F6"),
        ],
        cloning_sites=["NheI", "BamHI", "EcoRI", "EcoRV", "BstXI", "NotI", "XhoI", "XbaI", "ApaI", "HindIII", "KpnI"],
        source="library",
    ))

    # pET-28a — bacterial expression with His-tag
    backbones.append(PlasmidBackbone(
        name="pET-28a(+)",
        description="E. coli T7 expression vector (5,369 bp). N-terminal His-tag, T7 promoter, kanamycin resistance.",
        sequence="ATCCGGATATAGTTCCTCCTTTCAGCAAAAAACCCCTCAAGACCCGTTTAGAGGCCCCAAGGGGTTATGCTAGTTATTGCTCAGCGGTGGCAGCAGCCAACTCAGCTTCCTTTCGGGCTTTGTTAGCAGCCGGATCTCAGTGGTGGTGGTGGTGGTGCTCGAGTGCGGCCGCAAGCTTGTCGACGGAGCTCGAATTCGGATCCGATATCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCG" + "T" * 100,
        features=[
            PlasmidFeature(label="T7 promoter", feature_type="promoter", start=1, end=50, color="#8B5CF6"),
            PlasmidFeature(label="His-tag", feature_type="tag", start=50, end=80, color="#F59E0B"),
            PlasmidFeature(label="MCS", feature_type="cloning_site", start=80, end=200, color="#F59E0B"),
            PlasmidFeature(label="KanR", feature_type="resistance", start=500, end=1300, color="#10B981"),
            PlasmidFeature(label="pBR322 ori", feature_type="ori", start=1300, end=1800, color="#3B82F6"),
        ],
        cloning_sites=["NcoI", "NdeI", "BamHI", "EcoRI", "SalI", "HindIII", "NotI", "XhoI", "NheI"],
        source="library",
    ))

    # pGEM-T — TA cloning vector
    backbones.append(PlasmidBackbone(
        name="pGEM-T Easy",
        description="TA cloning vector (3,015 bp). T7 and SP6 promoters flanking MCS within lacZ, ampicillin resistance.",
        sequence="GGGCGAATTGGGCCCGACGTCGCATGCTCCCGGCCGCCATGGCGGCCGCGGGAATTCGATTTAAATCTAGAGTCGACCTGCAGGCATGCAAGCTTGAGTATTCTATAGTGTCACCTAAATAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACAT" + "A" * 100,
        features=[
            PlasmidFeature(label="T7 promoter", feature_type="promoter", start=1, end=30, color="#8B5CF6"),
            PlasmidFeature(label="SP6 promoter", feature_type="promoter", start=180, end=210, strand="-", color="#8B5CF6"),
            PlasmidFeature(label="MCS", feature_type="cloning_site", start=30, end=180, color="#F59E0B"),
            PlasmidFeature(label="AmpR", feature_type="resistance", start=350, end=1200, color="#EF4444"),
        ],
        cloning_sites=["EcoRI", "SacI", "BstXI", "NotI", "SalI", "NcoI", "BamHI", "SpeI", "ApaI"],
        source="library",
    ))

    return backbones