Choosing a genome browser for your organism…

There are a number of genome browsers out there–we’ve covered that a number of times.  And there are always new ones coming along.  With the onslaught of sequence data we’re about to get from high-throughput sequencing, more and more research groups, communities, and individuals are going to need to choose a genome browser to use to display their data.

One time I stumbled across the survey results for a group that was choosing a new platform to display their community’s data: MaizeGDB.  I wrote about it then because I thought it was interesting, and because I know people are facing this pretty regularly now.  We get asked.  But since that time they have progressed, implemented, and they wrote up their experience.  It’s now been published in Database.

It’s a pretty straighforward paper.  They describe their needs and their assessment of the resources their community had and used.  They surveyed likely users to see what they wanted, and how they felt about the pieces that already existed.  One piece they specifically noted–when asked, many users did not say they used Ensembl, but the Ensembl software was the foundation of one of the items they did say they used.  MaizeGDB writes:

This result shows that users may not be aware of the underlying browser software that the various web sites use.

Ah, yeah.  Here’s another thing this shows: database end users are definitely not thinking about browser software the same way database developers are.  And I do not mean end users are stupid.  They just do not think about this stuff the way software providers think they do.  We keep trying to tell providers this.  It’s not always well received.

So anyway, they move on to assess the candidates for their new implementation.  The focus on Ensembl, GBrowse, Map Viewer, UCSC Genome Browser, and xGDB.  They describe the framework, possibilities, and limitations of each for their purposes.  I think this is a nice look at the various options that lots of people considering the issue should find useful.  They also address that there are other browser that have since, or may still, come along in the future that could be considered, but at the time these were the focus.

They go on to describe their implementation experience.  They seem pleased with it.  And they highlight a one of their favorite pieces, a Locus Lookup tool, that they have added as well.  It sounds like it’s serving their community really nicely.

This is a highly useful paper for the people in the market for genome browsers.  It’s not for everyone, for sure.  Well, at least not yet.  But your day is coming. You’ll need a browser eventually….

You can check out their GBrowse implementation at: http://gbrowse.maizegdb.org/

And if you are interested you can see our free GBrowse training suite here: http://www.openhelix.com/gbrowse

References:
Sen, T., Harper, L., Schaeffer, M., Andorf, C., Seigfried, T., Campbell, D., & Lawrence, C. (2010). Choosing a genome browser for a Model Organism Database: surveying the Maize community Database, 2010 DOI: 10.1093/database/baq007

Andorf, C., Lawrence, C., Harper, L., Schaeffer, M., Campbell, D., & Sen, T. (2010). The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps Bioinformatics, 26 (3), 434-436 DOI: 10.1093/bioinformatics/btp556

EDIT: added links to a couple of older blog posts, should have had them in before….

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