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Data sources and licences
Where the reference data in Plasmole comes from, who to credit and under which licence.
Plasmole's reference data — the feature library auto-annotation searches, the enzyme and primer catalogues — comes from public databases and published papers. This page says which, under which licence, and who to credit. Every row in the feature library records its own source, that licence and the date it was retrieved, so a feature you see on a map can be traced back to the record it came from.
If you publish work that used an annotation from Plasmole, cite the source of that feature, not Plasmole.
Feature library
| Source | What it contributes | Licence | Credit |
|---|---|---|---|
| pLannotate | The feature set auto-annotation searches today, which the sources below are replacing. See the note under this table | Code GPLv3; the feature set's own terms are unsettled | McGuffie MJ, Barrick JE. pLannotate: engineered plasmid annotation. Nucleic Acids Res. 2021;49(W1):W516–W522. doi:10.1093/nar/gkab374 |
| GenoLIB | Common plasmid features: markers, origins, promoters, terminators, binding sites | CC BY 4.0 | Adames NR, Wilson ML, Fang G, Lux MW, Glick BS, Peccoud J. GenoLIB: a database of biological parts derived from a library of common plasmid features. Nucleic Acids Res. 2015;43(10):4823–4832. doi:10.1093/nar/gkv272 |
| FPbase | Fluorescent-protein identity and cross-references. The coding DNA itself comes from the INSDC record each entry cites | Open data, credit the authors | Lambert TJ. FPbase: a community-editable fluorescent protein database. Nat Methods. 2019;16(4):277–278. doi:10.1038/s41592-019-0352-8. Each protein also carries its own primary citation |
| UniProtKB/Swiss-Prot | A curated set of coding sequences no other source here covers. Protein identity from Swiss-Prot, DNA from the INSDC record the entry cites | CC BY 4.0 | The UniProt Consortium, Nucleic Acids Res. 2025;53(D1):D609–D617 |
| Rfam 15.1 | RNA families a plasmid or viral vector carries: copy-control antisense RNAs, U6, ribozymes, IRES elements, packaging signals | CC0 1.0 | Ontiveros-Palacios N, et al. Rfam 15. Nucleic Acids Res. 2025;53(D1):D258–D267 |
| SEVA | The SEVA modules — markers, origins, oriT, terminators — read from the authors' own GenBank depositions | GenBank records; INSDC data carries no redistribution restriction | Silva-Rocha R, et al. Nucleic Acids Res. 2013;41(D1):D666–D675. doi:10.1093/nar/gks1119 |
| GenBank / INSDC | The nucleotide records the FPbase and Swiss-Prot rows are sliced from, and the vector elements read from each vector's own record (polylinkers, AAV2 ITRs, the lentiCRISPR filler, short marks such as the pol III terminator), cited by accession and coordinates | No restriction on redistribution | NCBI GenBank |
The set auto-annotation searches today is being replaced. Most of what auto-annotation currently finds comes from pLannotate's feature set. pLannotate's code is GPLv3, but its feature set has a history its authors describe in the paper above: it came from SnapGene's database, which was first built as GenoLIB, and was then cross-referenced against 195,426 GenBank files from Addgene that carried SnapGene's automated annotations.
The replacement is built only from the other sources in this table, under the licences in this table. It is loaded and not yet switched on: it becomes the default once we have measured that it finds what the current set finds, and this page will say so the day that happens. Rfam's rows, and most of the FPbase, Swiss-Prot, SEVA and GenoLIB rows, are in that pending set and are not searched yet. Where a row Plasmole searches today carries a name and bases that one of those sources also holds, the row is already credited to that source.
Plasmole has never used the Benchling, Geneious or ApE feature databases, and does not redistribute Addgene's bulk plasmid data. Those sets are either proprietary or licensed for non-commercial use only.
Restriction enzymes
The enzymes Plasmole ships come from Biopython's Bio.Restriction set, pinned to the set matching REBASE release 610 and retrieved on 13 October 2026. Every enzyme records that release.
| Source | What it contributes | Licence | Credit |
|---|---|---|---|
Biopython Bio.Restriction |
The enzyme set itself: names, recognition sites, cut positions, isoschizomer groups and supplier names | Biopython licence (MIT-style) | Cock PJA, et al. Bioinformatics. 2009;25(11):1422–1423 |
| REBASE | The database that set is built from, which is why it is cited here | REBASE's own data files are published "All rights reserved", and New England Biolabs' Terms of Use permit non-commercial individual reference. Plasmole does not redistribute REBASE's data files; it uses the enzyme set as Biopython distributes it | Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE: a database for DNA restriction and modification. Nucleic Acids Res |
Plasmole carries no NEB reaction-condition data. No buffer activity, optimal buffer, incubation or heat-inactivation temperature, star activity, Dam, Dcm or CpG sensitivity, catalogue number, Time-Saver or HF designation. Earlier versions of Plasmole showed some of these. They were removed in October 2026, and the database now refuses such a value outright rather than relying on convention.
313 of the 1,015 enzymes have no cut position, because REBASE gives none. Plasmole shows their recognition site and never builds a fragment from it, rather than guessing where they cut.
Primers
Common primer sequences are slices of public GenBank records, cited by accession and coordinates. Vendor primer lists (Addgene, Quintara, Eurofins) are published under non-commercial terms, so none is copied — only vendor names survive, as aliases on the binding site.
Tools Plasmole runs
| Tool | What it does | Licence |
|---|---|---|
| NCBI BLAST+ | Sequence search and auto-annotation | Public domain (US government work) |
| MUSCLE v5 | Multiple sequence alignment | GPLv3 |
| Primer3 | Primer design | GPLv2 |
| Biopython, pydna | Sequence handling and cloning simulation | Biopython licence, BSD |
Your own data
Your sequences, entries and files are yours. Nothing you upload is added to the reference data above, and nothing you upload is used to train a model. See /docs/data-export-support for export, and the privacy policy for how your data is handled.
Something missing or wrong? Email [email protected].