Plasmid Annotator: Detect Features on a Map
Auto-detect promoters, tags, origins and resistance markers in a plasmid, then run a deep scan against pLannotate's full feature databases.
Paste a plasmid or DNA sequence to auto-annotate it. The instant quick scan matches a bundled library of short signature sequences on both strands, identifying promoters, operators, RBS and Kozak sites, affinity tags, origins of replication, resistance markers and MCS clusters. For a far more thorough pass, run the deep scan: it searches pLannotate's full open-source databases (SnapGene common features, Swiss-Prot, FPbase, Rfam) with BLAST, DIAMOND and Infernal, finds variants and truncated fragments the signature library misses, and reports a percent identity and reference coverage for every hit so you can judge a weak match. Either way, detected features are drawn on a circular and linear plasmid map online, with a table of type, coordinates, strand and length.
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▸Display: circular + linear · “My construct”
Which backbone is it?
Annotation says what the parts are; it does not say what the plasmid IS. This screens the same sequence against a curated set of common cloning, expression and BAC backbones and reports which one it resembles, how much of it is accounted for, and whether the coverage pattern looks like a chimera.
Top-ranked backbones to align and list. Default 5.
Each candidate is aligned against your whole sequence, so a screen takes a moment rather than updating as you type.
Paste a plasmid above, and this screens it against the curated vector set.
Both at once, and what neither explains
The two crossed together: recognized features on one axis, backbone identity on the other, and — the part that is usually the point — the regions of your plasmid that neither the feature library nor the closest backbone accounts for.
Paste a plasmid above, and this crosses its annotation with its backbone. Works best on a complete plasmid — a partial read matches a backbone over less of its length and inflates the unexplained regions.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
How to use the Plasmid Annotator tool
- 1Paste a plasmid or DNA sequence into the "DNA sequence" box, or click one of the two examples — "Load example" for a 3 kb plasmid with an insert, "Tag & promoter example" for a short construct carrying T7, lac, RBS, His6, FLAG and an MCS; the quick scan reruns automatically a moment after you stop typing.
- 2Click "Run deep scan" to search pLannotate's full databases instead. It takes a few seconds; use the "Quick scan" / "Deep scan" toggle to compare the two result sets.
- 3Set a "Construct name" and pick "Circular + linear", "Circular only" or "Linear only" from the View dropdown.
- 4Read the summary tiles and the colored type chips, then check the features table for each hit's type, start, end, strand and length — deep-scan rows also show percent identity, reference coverage, source database, and "partial" or "crosses origin" badges.
- 5With a circular view showing, save the map from the Figure button as SVG, PNG or PDF, or press Share to copy a link that reopens the same construct.
Frequently asked questions
Which features can the Plasmid Auto-Annotator detect?
It looks for common cloning elements using short signature sequences: promoters (T7, T3, SP6, lac, tac, araBAD, CMV, EF-1a, SV40), the lac operator and CAP site, Shine-Dalgarno and Kozak sequences, affinity/epitope tags (His6, FLAG, HA, Myc, Strep-II, V5, T7), origins of replication (ColE1/pMB1, f1, SV40), antibiotic-resistance markers (AmpR/bla, KanR, CmR, TetR), universal sequencing primers (M13, T7) and a pUC-style multiple cloning site.
How does detection work — is it exhaustive?
There are two scans. The quick scan flags a feature by matching a short, characteristic signature (roughly 50 bp or less) on both strands, tolerating IUPAC ambiguity codes; because the library is curated and the signatures are short, variants, synonymous codon choices and anything outside the library will not be recognized. Treat it as a fast first pass. The deep scan is the thorough option: it runs BLAST, DIAMOND and Infernal against pLannotate's full databases, so it finds variants and partial features the signature library misses — but because it reports imperfect matches too, check the percent identity column before trusting a low-scoring hit.
Does it scan both DNA strands?
Yes. Every signature is searched on the forward strand and as its reverse complement, so features encoded on the antisense strand are reported with forward-strand coordinates and a minus (reverse) strand label.
Can I run this from code?
Yes — both plasmid_annotate and plasmid_deep_annotate are callable from the REST API and MCP server.
What is the deep scan, and how is it different?
The deep scan calls pLannotate, an open-source reimplementation of the common-features auto-annotation you get from desktop tools like SnapGene, cross-referenced against roughly 195,000 SnapGene-annotated plasmids deposited at Addgene. Instead of matching short signatures it aligns your sequence against full feature databases — SnapGene common features, Swiss-Prot, FPbase and Rfam — using BLAST, DIAMOND and Infernal. On pUC19 it recovers features the quick signature scan has no entry for at all, such as the RNAI transcript, the bom site and the rop coding sequence. It takes a few seconds rather than being instant.
Why does a deep-scan feature show less than 100% identity, or a "partial" badge?
Deep scan reports imperfect and truncated matches rather than only exact hits, which is what lets it recognize engineered variants. Identity is the percent match over the aligned region; coverage is how much of the reference feature is present, and a "partial" badge means only part of it is. A hit at 99-100% identity with full coverage is a confident call; something in the 60-70s may be a distant homolog rather than the named feature, so treat it as a lead to check, not a conclusion.
Is there a limit on the deep scan?
Yes. Deep scan runs a multi-second database search on a shared service, so it is capped at 150,000 bp per sequence — which covers every plasmid, including large expression constructs, and takes in cosmids, fosmids and large viral genomes as well — and is rate limited per user. Normal interactive use will not hit the limit; if you do, the error tells you how long to wait, and the quick scan stays available and unmetered. The sequence must also be A, C, G, T or N: other IUPAC ambiguity codes are rejected rather than silently dropped, because the search engines discard them and every reported coordinate after such a base would be shifted.
More
Guides
Related tools
Type or paste a sequence and edit it directly — every feature remaps live as you insert, delete, or replace bases, with undo/redo and GenBank import/export.
Render a circular or linear map with restriction sites.
Paste a GenBank record and see an annotated circular or linear map with a feature table.