Plasmid Auto-Annotator — Detect Features on a DNA Map
Auto-detect promoters, tags, origins and resistance markers in a plasmid and render them on a map.
🔒 Local processing — pasted sequences are not uploaded
Paste a plasmid or DNA sequence and let the Plasmid Auto-Annotator scan it for common cloning features. It searches both strands with a bundled library of short, reliable signature sequences — promoters (T7, SP6, T3, lac, tac, CMV, EF-1a, SV40), operators, ribosome binding and Kozak sites, affinity and epitope tags (His6, FLAG, HA, Myc, Strep-II, V5, T7), origins of replication (ColE1/pMB1, f1, SV40), antibiotic-resistance markers (AmpR, KanR, CmR, TetR) and multiple cloning sites — then draws every hit on an interactive circular and linear map alongside a sortable feature table. It runs entirely in your browser, so no sequence is uploaded.
0 bp
Detection uses a bundled library of short signature sequences and is not exhaustive — variants, synonymous codon choices and elements outside the library will not be flagged. Treat the map as a fast first pass, not an authoritative annotation.
How to use the Plasmid Annotator tool
- 1Paste a plasmid or DNA sequence (plain text or FASTA), or click Load example.
- 2Optionally name your construct and choose circular, linear, or both views.
- 3Read the auto-detected feature list and colored map, then share a link or export the figure as SVG/PNG.
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?
- No. Each feature is flagged by matching a short, characteristic signature (roughly 50 bp or less) on both the forward and reverse strand, with IUPAC ambiguity codes tolerated. Because the library is curated and signatures are short, variants, synonymous codon choices and elements not in the library will not be recognized. Treat the map as a fast first pass, not an authoritative annotation.
- 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.
- Is my plasmid sequence uploaded?
- No. Feature detection and rendering run locally in your browser, so the sequence is not uploaded to SeqBench.