JBrowse: A next-generation genome browser

  1. Mitchell E. Skinner1,
  2. Andrew V. Uzilov1,
  3. Lincoln D. Stein2,
  4. Christopher J. Mungall3 and
  5. Ian H. Holmes1,3,4
  1. 1 Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA;
  2. 2 Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada;
  3. 3 Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

    Abstract

    We describe an open source, portable, JavaScript-based genome browser, JBrowse, that can be used to navigate genome annotations over the web. JBrowse helps preserve the user's sense of location by avoiding discontinuous transitions, instead offering smoothly animated panning, zooming, navigation, and track selection. Unlike most existing genome browsers, where the genome is rendered into images on the webserver and the role of the client is restricted to displaying those images, JBrowse distributes work between the server and client and therefore uses significantly less server overhead than previous genome browsers. We report benchmark results empirically comparing server- and client-side rendering strategies, review the architecture and design considerations of JBrowse, and describe a simple wiki plug-in that allows users to upload and share annotation tracks.

    Footnotes

    • 4 Corresponding author.

      E-mail ihh{at}berkeley.edu; fax (510) 642-5835.

    • [The JBrowse source code (freely licensed), live demonstrations, mailing list, documentation, bug-tracking, and virtual machine images are available at http://jbrowse.org/.]

    • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.094607.109.

      • Received April 1, 2009.
      • Accepted June 16, 2009.

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