I’ve released a new version of XPlasMap, version 0.96 (asymptotically approaching a non-beta release). XPlasMap 0.96 can be downloaded here, and the XPlasMap home page is here.

XPlasMap is a DNA drawing program for MacOSX (MacOS10.4 and up only for this release; a slightly older version runs on MacOS10.3 [download XPlasMap10.3 here] ) It draws plasmid maps with all the features you’d expect (genes, multiple cloning sites, restriction sites, and so on), pretty much interactive. It also draws linear DNA maps and will draw maps by importing directly from GenBank files. It will also import from FastA files; for both FastA and GenBank sequence it will map out restriction sites (slowly! –it’s no competition for specialized restriction mapping programs like EnzymeX or the venerable DNA Strider) and identify open reading frames (again, slowly). Maps can be saved as .xpmp files (which is simply an XML format; I wanted to make sure that the information in the maps would remain accessible and in a non-proprietary format), or exported to PNG or JPG.

Here’s a sample plasmid map, for Invitrogen’s pTracerCMV2 (click on the image for a larger version):

pTracerCMV2 - XPlasMap

And here’s a sample of a linear DNA map (click for a larger version). This is the human genomic major histocompatibility region, imported directly from a GenBank file (3.7 million base pairs). The class I region is highlighted in orange, class III region in green, and class II region in blue.

HLA Genomic - XPlasMap

The 0.96 release is mainly a bug-fix release; there are preliminary versions of a couple of new features, with annotations being the main new feature.

New features:

  • Annotations
  • “Plasmid comment” is now free-form text (can be moved and edited)
  • (Preference option) Common actions on a toolbar

Bugfixes:

  • Improved print resolution
  • Fixed: Intermittent Clear Recent Files bug
  • Fixed: JPG and PNG exports use a large canvas with image only in one corner
  • Fixed: Error on copying in reverse
  • Fixed: Font preferences not always honored
  • Fixed: Going from linear to circular, genes disappear
  • Fixed: Contextual menus occasionally not responding
  • Fixed: Show/Hide enzyme lost after save
  • Fixed: Genes with no name disrupt drawing
  • Fixed: Freeze in Cut Plasmid
  • Fixed: Hiccup if no Preference file

Assorted other bugfixes and UI improvements

XPlasMap only runs on Macs (though it’s written in Python/wxPython, which means that it should be a straightforward recompile to run on other OSes — but I only use Macs so haven’t tried). I also wrote a much more primitive (but still rather attractive) on-line plasmid-mapping program that is OS-independent: Savage Plasmids draws SVG maps and exports to Postscript. Unfortunately browser support for SVG is still at best spotty and hasn’t improved much over the past couple of years, as far as I know.  SVG will do interactive, but I’ve never got around to making the program interactive (and likely never will, now), so XPlasMap really makes much nicer maps.