genepad-commonfeatures

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A library of common plasmid features for quickly annotating standard elements (promoters, resistance markers, origins of replication, tags, fluorescent proteins, terminators, recombination sites, ...) in plasmid mapping software.

The library currently contains 314 features in 20 categories (full list in docs/FEATURES.md):

Category	Count	Examples
antibiotic_resistance	20	AmpR, KanR/Neo, KanR (Tn903/Tn5), nptIII, CmR, TetR, ZeoR, HygR, PuroR, BlastR, SpecR, GmR, ApraR, NatR, EryR, DfrB, blaSHV, aac(6')-Ib, bar
origins	12	pUC, ColE1/pMB1, p15A, pSC101, f1, R6Kγ, CloDF13, RK2 oriV, RSF1010, pBBR1, oriT, bom
bacterial_promoters	16	T7, SP6, T3, lac, lacUV5, trc, tac, araBAD, rhaBAD, λpL/pR, T5, EM7, AmpR/cat/lacI promoters
bacterial_terminators	7	T7Te, rrnB T1/T2, rrnB, λt0, T3, ECK120029600
bacterial_regulatory	17	lacI, araC, tetR, cI857, Cre, Flp/FLPo, Dre, φC31 integrase, lacO, tetO, T7lac, sacB, ccdB, rop
mammalian_promoters	37	CMV, SV40, EF1α, EFS, PGK, RSV, CAG, CBh, UbC, hU6, H1, 7SK, TK, TRE3G, hSyn, CaMKIIα, GFAP, TBG, MCK, MHCK7, ALB, Desmin, Myh6/7, MBP, MOG, PLP1, TH, mDlx, NSE, Pcp2, RHO, Tie2, CDH5, PDGFB, ApoE, hTERT
mammalian_terminators	5	SV40 early/late polyA, BGH polyA, HSV TK polyA, synthetic polyA
mammalian_regulatory	10	SV40 ori, EMCV/CrPV IRES, WPRE, TRE-Tight, oriP, cHS4 insulator, tTA, chimeric intron
yeast_elements	19	GAL1p, ADH1p/t, CYC1t, TEF1p/t, TDH3p, PGK1p/t, kanMX, CEN6/ARS4, 2µ ori, URA3/LEU2/HIS3/TRP1/MET15, 5xUAS
plant_elements	8	CaMV 35S p/t, NOS p/t, T-DNA borders, NPTII, OCS t
insect_elements	4	polh, p10, OpIE2, hr5
igem_parts	30	Anderson promoters J23100–J23119, RBS B0030–B0034, B0015 terminator, RFC[10] prefix/suffix/scar
aav_elements	18	AAV2 ITR, hGH polyA, rBG polyA, cap (VP1) 2/5/6/8/9/rh10/rh74/10HB, AAV2 Rep78/68/52/40, AAP2/5, MAAP2
viral_elements	15	HIV-1 5′LTR, 3′SIN LTR, Ψ, RRE, cPPT/CTS, MSCV/MMLV/SFFV/RCAS LTR, WPRE3, HBV enhancer I/II, HCV/PV IRES, Ad5 Ψ
protein_tags	35	6x/8xHis, FLAG, HA, Myc, V5, VSV-G, GST, MBP, SUMO, TrxA, Twin-Strep, AviTag, SpyTag, 2A peptides, TEV/3C/Thrombin/EK/FXa sites, pelB/ompA/Igκ leaders, Rev NES
fluorescent_proteins	14	EGFP, ECFP, EYFP, Venus, mCerulean, mCherry, mRFP1, tdTomato, DsRed2, mKate2, mScarlet-I, mTagBFP2, sfGFP, mNeonGreen
reporter_enzymes	7	luc+, Renilla, NanoLuc, SEAP, lacZ (full-length/α), uidA
recombination_sites	17	loxP, lox2272, lox5171, lox511, FRT, F3, Gateway attB/P/L/R, φC31 attB/attP, Bxb1 attP
primer_binding_sites	12	M13 fwd/rev, T7, T7term, SP6, T3, CMV-F, BGH-R, pGEX 5′/3′, pBAD-F/R
misc_features	11	Kozak, pUC19 MCS, SpCas9, dCas9, nCas9, SpCas9-HF1, LbCas12a, CasRx, sgRNA/crRNA scaffolds

Repository layout

data/
  sources/        # feature source definitions (one JSON shard per topic, hand-maintained)
  features.json   # generated canonical library (do not edit by hand)
  genbank_cache/  # cached NCBI source records
scripts/
  fetch_features.py   # extract feature sequences from NCBI records -> data/features.json
  export.py           # data/features.json -> genbank/ and fasta/
  verify.py           # quality gate: alphabet / reading frames / reference-sequence checks
genbank/          # GenBank files by category (import into SnapGene / Benchling / ...)
fasta/            # FASTA files by category
docs/FEATURES.md  # full feature list (with sources and notes)

Usage

Import the .gb files for the categories you need from genbank/ into your plasmid software as a common-features library, or use the sequences in fasta/ for BLAST/alignment-based annotation.

Regenerating

python scripts/fetch_features.py   # needs NCBI access; uses data/genbank_cache/
python scripts/export.py
python scripts/verify.py           # quality gate: alphabet / frames / reference checks

Contributing a new feature

1. Add an entry to the appropriate shard in data/sources/:
   • NCBI-extracted (preferred): give the accession plus a feature selector (match qualifier regexes, or coords);
   • Curated (only for standard public sequences <150 bp): give the sequence and state the reference.
2. Run fetch_features.py, export.py, then verify.py; submit only when all three pass.

Data provenance

Every feature records its source (NCBI accession + reference record name, or the origin of a standard public sequence) in the source field of each entry in data/features.json.

License

Released under the MIT License. The feature sequences themselves are factual data in the public domain; the curation, structure and scripts of this repository are covered by the MIT license.