Tuesday, December 02, 2008

Browsing genomes

I may as well come clean and admit that I'm developing a genome browser. What? Another genome browser? Why? You may well ask these questions. Well, it's a long story. But here is a completely non-exhaustive list of existing genome browsers.

Note: updated in Sept. 2009 to reflect the fact that everyone and their uncle built a genome browser this past couple of years. See Brother, can you spare a genome browser?

Note: updated again in May of 2010 and again in Feb 2011 to add Savant.


  1. Hi there, I'm the developer of the X:Map database and website, and I can't wait to see what you come up with :)

    Genome browsers are a really interesting branch of user interface design in my opinion, as the data set is so huge, and people are split between those who want an extreme close-up view of a specific area, and those who want to be able to see a general overview of a region (and the surrounding features).

    As you can tell from our site, we went more for the latter ;-)

    Good luck with it!!


  2. Hi Tim,

    Thanks for the encouragement. X:Map is very cool - I really like the approach of rendering the tiles in R. (That's how you guys do it, right?)


  3. We have an R package 'exonmap' for doing data analysis, but the actual tiles are pre-rendered with a Java app I wrote.

  4. Nice compilation of browsers. Don't forget Ensembl.

    Have you released your own browser yet? Do you still like protovis?

  5. Hi Steve,

    I like protovis a lot. I made a little experimental prototype of a genome browser in protovis. It's not too likely that I'll follow up on that, but I'm using protovis for other purposes in my current project.

    My genome browser is released on the Gaggle Genome Browser website and written up in a paper as well.