News/MaizeGDB: Choosing GBrowse

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Database Paper

A paper, "Choosing a genome browser for a Model Organism Database: surveying the Maize community," by the MaizeGDB team has been published in Database. To prepare for the availability of a reference genome, MaizeGDB surveyed their community to assess genome visualization needs. This paper summarizes the survey and MaizeGDB's review of available browsers, and describes why they chose GBrowse. The paper finishes by describing how they implemented GBrowse, including the locus lookup tool (described here), a MaizeGDB extension that uses maize's extensive physical and genetic mapping data to localize genomic regions in GBrowse. This is a great paper for anyone considering which genome browser to use.

Database Journal

I'd also like to highlight the journal the paper appears in: Database: The Journal of Biological Databases and Curation. "Biological Databases and Curation" are what GMOD is about and many of the papers cover issues and resources that are widely applicable in the GMOD community. The current issue also includes papers on community annotation using wikis, and a report on best practices in genome annotation from the ISB 3rd International Biocuration Conference. Database is an open access publication, making it an even better match for GMOD.

Dave Clements
GMOD Help Desk

Posted to the GMOD News on 2010/04/19