Plasmid map

Input. Paste or open a GenBank (.gb) record, FASTA, or a bare DNA sequence. GenBank features are read from their locations (including complement(…) and origin-spanning join(…,1..n)) and named from /label, /gene, /product, or /note. Choose circular or linear topology. The sample is the real pUC19 sequence (GenBank L09137.2, 2686 bp; Yanisch-Perron, Vieira & Messing 1985) with its standard features — lacZα 146–469, MCS 396–452, lac promoter and operator, CAP site, pMB1 ori 867–1455, AmpR 1626–2486 and its promoter — each placed by sequence search.

Map. Features are drawn as arcs (arrowheads show the strand); overlapping features go on separate rings. Restriction sites come from the sequence tool's enzyme list (about 60 common enzymes, top-strand cut positions); single cutters are bold, and 1–2 cutters adds double cutters. Click a feature to select it or an enzyme to add a digest lane. ⛶ Full screen (or F) gives the map the whole screen — the browser’s full screen where it is allowed, otherwise a full-window layer (iPhone); the sequence panel moves beside it and ◫ Panels hides it. Escape leaves.

Features. Edit names, types, coordinates (1-based, inclusive) and strand; a start after the end means the feature crosses the origin. Copy a feature’s DNA (in its own orientation) or protein. Auto-annotate looks for: AmpR (bla), KanR (Tn903 aph), CmR (cat), EGFP and lacZα (signature start, extended to the first in-frame stop); the pMB1 ori and AmpR promoter (fixed lengths from pUC19); lac promoter, lac operator, CAP site, T7, T3 and SP6 promoters and M13 primer sites (exact matches); and a multiple cloning site, reported where four or more unique 6-bp cutters fall within 80 bp. Matches are exact, so variant or codon-optimised genes are missed.

Digest. One lane per digest; combine enzymes with +. Fragments include coordinates. The gel places bands log-linearly between the ladder extremes (1 kb, 1 kb Plus, or 100 bp ladder sizes) with brightness proportional to mass; it ignores star activity, methylation (e.g. Dam-blocked XbaI or ClaI sites) and partial digests. An uncut circular plasmid is shown at about 0.7× its size to mimic supercoiled DNA, which really varies with gel and voltage.

Export. GenBank (with /label and /note qualifiers), FASTA, and the map as SVG or PNG. For translation, ORFs and primer design use the sequence tool.