Choosing a genome browser for a Model Organism Database: surveying the Maize community

Taner Z. Sen, United States Department of Agriculture
Lisa C. Harper, United States Department of Agriculture
Mary L. Schaeffer, United States Department of Agriculture
Carson M. Andorf, United States Department of Agriculture
Trent E. Seigfried, United States Department of Agriculture
Darwin A. Campbell, United States Department of Agriculture
Carolyn J. Lawrence, United States Department of Agriculture

This article is from Database 2010 (2010): baq007, doi:10.1093/database/baq007. Posted with permission.

Abstract

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly.