Home / Science / Molecular and cell biology / Molecular biology / Plasmid map viewer and editorTool #170

Plasmid map viewer and editor: open a GenBank file, draw a circular map, edit features, download SVG

Open or paste a GenBank or FASTA file and get a clean circular or linear plasmid map with feature arrows, single-cutter sites and a size ruler. Rename, recolour, move or add features, move the origin, and download the map as SVG, PNG or PDF and the plasmid as GenBank.

Keep it one tap away for everyday use.

Bookmark Plasmid map viewer and editor?

Press Ctrl + D now. Your browser opens its own bookmark box, where you choose the name and folder.

  1. Open
  2. Map
  3. Edit
  4. Download
Nothing is uploadedWorks offline once open

Plasmid

GenBank (.gb, .gbk, or a file from most plasmid editors) or FASTA up to 20 MB; the first record is used, up to 1 million bases. The file stays on your device. Changing this box starts again from it, so download your edits first. The example is random made-up sequence with made-up features.

Map

Download

Features

Edit a name, type, position, strand or colour and the map follows. Start can be larger than end on a circular plasmid for a feature that crosses base 1. Features made of several pieces keep their pieces; change those in the GenBank text. Untick a feature to hide it from the map.

Move the origin

Moving the origin renumbers the sequence and every feature; features that cross the new base 1 are split into two pieces, and pieces that meet again are joined.

What it does

A plasmid map shows at a glance where the genes, promoters, origin and handy cut sites sit on a circle of DNA. This page draws one from your own file, in your browser:

  • Reads GenBank files, the format most plasmid editors and sequence databases export, including features in several pieces (join), on the reverse strand (complement), crossing base 1, and with partial ends (< and >). FASTA or plain sequence also works, with no features.
  • Circular or linear map. Features become arrows that point along their strand. Overlapping features stack on inner tracks, labels are spread apart so they don’t overlap, and a ruler shows positions.
  • Enzyme sites. Shows where the 12 classic enzymes cut once (the usual choice for cloning), all their sites, or none.
  • Edit. Rename, retype, recolour, move or hide any feature, add new ones, and move the origin so any base becomes base 1.
  • Download. The map as SVG (for posters and papers, sharp at any size) or in a PNG, PDF or Word report with a feature table, and the edited plasmid as a GenBank file.

How to use it

  1. Open. Open a .gb or .gbk file, or paste the text. The first record is used.
  2. Map. Choose circular or linear and which enzyme sites to show.
  3. Edit. Change features in the list under the map. On a circular plasmid, a start larger than the end makes a feature that crosses base 1.
  4. Download. Save the map and the GenBank file.

Worked example

The example, pDemo1, is 3,000 bp of random made-up sequence with seven made-up features: a promoter, a forward primer site, a forward gene called reporterX (201..1106), a terminator, an origin (1301..1889), a reverse-strand marker gene (complement(1981..2841)) and a cloning site that crosses base 1, join(2961..3000,1..40). A full-length source feature is listed but hidden.

Seven of the 12 classic enzymes cut it exactly once, among them EcoRV at 319, BamHI at 1,151 and HindIII at 2,211, and these are the enzymes you would try first to open this plasmid. XhoI, KpnI and NotI do not cut it at all. Type 1301 into Move the origin and the origin feature now starts at base 1, every other feature is renumbered, and the cloning site becomes one piece again because it no longer crosses base 1.

Tips

  • Colours are only for the map. The GenBank download keeps names, types, positions and notes, and other programs use their own colours.
  • Features with several pieces (such as a gene with introns) keep their pieces when you edit names and colours. Change their pieces in the GenBank text.
  • Large records such as whole bacterial genomes open, but a map with hundreds of features is crowded. Hide the ones you don’t need, or use the linear view.

FAQ

Is my sequence uploaded? No. The file is read and drawn in this page and never leaves your device.

Why is a feature missing? Features whose location points into another record (such as AB000001.1:1..50) cannot be drawn and are left out, with a note.

Can I open SnapGene .dna files? Not directly. Export GenBank from your editor first.

Where the numbers come from

  • GenBank reader and writer written by fibub from the public GenBank flat file layout. Feature positions, strands, joined pieces and qualifiers are checked in the tests against Biopython 1.88 SeqIO.
  • Recognition sites of the 12 built-in enzymes are textbook facts, shared with the restriction digest simulator. No enzyme database or supplier catalogue is copied.
  • The example plasmid pDemo1 is random made-up sequence with made-up features. It is not a real vector.

Standard scientific values, such as constants, atomic weights and melting points, are facts found in every textbook; we name where ours were checked. If you are an author or publisher and want a value, a credit or a table changed or removed, tell us and we will act quickly.

Last updated 2026-11-09.

Change log for Plasmid map viewer and editor

  1. Add #170 plasmid map viewer and editor (GenBank in and out, circular or linear map, SVG) Details on GitHub

Every change to fibub

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