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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #233491
Title: The MaizeGDB Genome Browser

Author
item Sen, Taner
item Andorf, Carson
item Campbell, Darwin
item Schaeffer, Mary
item Harper, Elisabeth
item Lawrence, Carolyn

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/3/2008
Publication Date: 1/12/2009
Citation: Sen, T.Z., Andorf, C.M., Campbell, D.A., Schaeffer, M.L., Harper, E.C., Lawrence, C.J. 2009. The MaizeGDB Genome Browser [abstract]. Plant and Animal Genome Conference Proceedings. p. 1.

Interpretive Summary:

Technical Abstract: MaizeGDB (http://www.maizegdb.org) is the community database for maize genetics and genomics. As part of an effort to develop MaizeGDB as a more sequence-centric resource, we implemented a genome browser based on information we gathered by surveying the community of maize geneticists. Based on community members’ impressions of existing genome visualization software and their list of desired functionalities, we chose to implement GBrowse. For the browser’s initial release, we collaborated with PlantGDB and MaizeSequence.org to populate the database. We also created links from the genomic elements to existing genetic data when possible. In this computer demonstration, we present the features of GBrowse (such as rubber-banding) and how the browser is connected with the rest of the MaizeGDB database and to off-site resources. As part of the implementation, unsequenced regions in the fingerprinted contigs are clearly identified and the imprecise positions of bin boundary markers are noted. These sorts of features provide maize researchers with an accurate picture of the maize genome, which enables researchers to spend less time on the computer and more time testing hypotheses at the bench.