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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE

Location: Corn Insects and Crop Genetics Research

Title: Choosing a Genome Browser for a Model Organism Database (MOD): Surveying the Maize Community

Authors
item Sen, Taner
item Harper, Elisabeth
item Schaeffer, Mary
item Andorf, Carson
item Seigfried, Trent -
item Campbell, Darwin
item Lawrence, Carolyn

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 9, 2010
Publication Date: April 15, 2010
Citation: Sen, T.Z., Harper, E.C., Schaeffer, M.L., Andorf, C.M., Seigfried, T.E., Campbell, D.A., Lawrence, C.J. 2010. Choosing a Genome Browser for a Model Organism Database (MOD): Surveying the Maize Community. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/baq007. p. 1.

Interpretive Summary: The Maize Genetics and Genomics Database (MaizeGDB) is the community resource for maize data and can be accessed online at http://www.maizegdb.org. The maize genome is being sequenced, and the outcomes of the sequencing project are being made available on a continuous basis. To present these outcomes, MaizeGDB is tasked with the implementation of a genome browser. Before choosing a genome browser, MaizeGDB surveyed the maize researchers about their preferences. Here, we provide the results of this survey and our rationale to choose GBrowse to satisfy the needs of maize researchers. The implementation of the genome browser and integrating it with the existing data available in MaizeGDB will enable researchers to have access to genomic information, help their research in understanding how the maize genome can be manipulated to obtain desired traits, and assist them in developing a better corn plant.

Technical Abstract: As the maize genome sequencing is nearing its completion, the Maize Genetics and Genomics Database (MaizeGDB), the Model Organism Database for maize, integrated a genome browser to its already existing Web interface and database. The addition of the MaizeGDB Genome Browser to MaizeGDB will allow it to efficiently represent maize research outcomes to the maize community and contribute to the efforts to produce maize plants with improved quality. Towards this end, instead of imposing a genome browser choice to its users, MaizeGDB has taken a rather unusual approach of surveying the researchers about the features they would like to have in a genome browser. The survey results indicate that the maize researchers want a genome browser that allows users to locate the needed data in the most accessible and fastest fashion, as well as intuitive tools that require short learning time. Here we provide a short review of major genome browsers, the detailed results of the survey we conducted, and our rationale to choose GBrowse to satisfy the needs of maize researchers. The MaizeGDB Genome Browser can be accessed at http://gbrowse.maizegdb.org/.

Last Modified: 9/23/2014
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