Introducing a new genome browser for WormBase

JBrowse

We are pleased to introduce a new genome browser that we are currently testing as a replacement for the current, long serving genome browser (GBrowse). The new browser, an implementation of JBrowse from the GMOD project, is currently available at wormbase.org/tools/genome/jbrowse/.  The new genome browser has a fast and pliable user interface; becoming oriented to the new browser should be relatively painless as it shares many design features in common with the current browser.

The new genome browser also has new functionality not available in the old one.  Key among these are (all of which are available from the genome browser’s file menu):

  1. Opening many types of data files (GFF, BAM, BigWig/BigBed, VCF), without having to upload them (so it’s *fast*).
  2. Creating combination tracks, where the contents of any two tracks can be combined using set or arithmetic operations.
  3. Making a sequence (DNA or amino acid) search track that will highlight when a motif is present (the search string can take the form of regular expressions–please let us know if you’d like help writing a regular expression).

Other useful features include the ability to “pin” a track to the top of the browser so it won’t scroll off the top of the page (simplifying visual comparisons with other open tracks), and a “full page” button that will open a new browser window where the genome browser takes up the full page.

Please try out the new browser and give us any feedback you can think of, either things you’d like to see, things you don’t like, whatever.