Plasmid map maker

Coordinates. Positions are 1-based and inclusive, as in GenBank. Position $p$ of a plasmid of $N$ bp sits at angle $\theta ={360}^{\circ }\times (p-1)/N$, clockwise from 12 o’clock, so base 1 is at the top. A feature from $s$ to $e$ covers $e-s+1$ bp; when $s>e$ it crosses the origin and covers $N-s+1+e$ bp. Forward-strand features point clockwise and reverse-strand (complement) features anticlockwise; an MCS or other feature without a direction is drawn as a plain band.

Layout. Features that overlap are placed on separate rings (longest first, each on the innermost free ring). Labels are split into the right and left halves of the circle, sorted by the height of their anchor, then pushed apart to at least one line of text and drawn on a larger circle with a leader line to the feature or site. Tick marks use a step of $1,2,2.5\text{ or }5\times {10}^k$ bp giving about 12 ticks.

GenBank import. The size comes from the LOCUS line (or the ORIGIN sequence). From the FEATURES table the tool reads CDS and gene (as genes, or resistance markers when the name or note mentions bla/AmpR, kan/neo, cat, tet, hph, zeo, bsd, puro or spec), promoter, rep_origin, terminator, regulatory promoters and terminators, and misc_feature entries labelled as an MCS or polylinker. A feature is named from /label, /gene, /product or /note. complement( ) gives the reverse strand; for join( ) the outermost positions are used, and a join that runs past the end (join(2600..2686,1..40)) becomes a feature crossing the origin. Source, primer_bind and −10/−35 boxes are left out to keep the map readable.

Restriction sites. The sequence is searched as a circle (sites spanning the origin are found) for 24 palindromic 6- and 8-base recognition sequences; the position given is the first base of the recognition site on the top strand.

Sources: pUC19 sequence and feature coordinates from New England Biolabs’ pUC19 GenBank file (neb.com, pUC19 GenBank), identical in sequence to GenBank L09137; Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 1985;33:103–119, doi:10.1016/0378-1119(85)90120-9.

The tool opens with pUC19, 2686 bp, with the features annotated by New England Biolabs (the promoters span NEB’s −35 to −10 boxes):

Every feature is on the reverse strand, so every arrow points anticlockwise. The MCS lies inside lacZα, so it goes on a second ring. Finding unique cutters in the sequence gives the polylinker sites EcoRI 396, SacI 402, KpnI 408, SmaI 412, BamHI 417, XbaI 423, SalI 429, PstI 435, SphI 441 and HindIII 447 (ten labels within 51 bp, spread apart by the label layout), plus NdeI 183, ScaI 2177 and AatII 2617 (XmaI cuts at the same site as SmaI). PvuI and PvuII cut twice.

Arc by hand. AmpR runs from 1626 to 2486: $2486-1626+1=861$ bp, and ${360}^{\circ }\times 861/2686={115.4}^{\circ }$. Its start sits at ${360}^{\circ }\times 1625/2686={217.8}^{\circ }$ clockwise from the top.

A feature across the origin. In a 5000 bp plasmid, a gene from 4800 to 300 covers $5000-4800+1+300=501$ bp; in GenBank it is written join(4800..5000,1..300).