ARS | Publication request: MaizeGDB's New Genome Browser Project

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: January 30, 2008
Publication Date: February 21, 2008
Citation: Sen, T.Z., Seigfried, T.E., Campbell, D.A., Schaeffer, M.L., Harper, E.C., Lawrence, C.J. 2008. MaizeGDB's New Genome Browser Project. In: 50th Maize Genetics Conference Proceedings, February 27-March 2, 2008, Washington, D.C. p. 61.

Technical Abstract: MaizeGDB (http://www.maizegdb.org) is the community database for maize genetics and genomics. Based upon the 2006 MaizeGDB Working Group Report (available at http://www.maizegdb.org/working_group.php) and the Allerton Report (http://www.maizegdb.org/AllertonReport.doc), it has become evident that the focus of MaizeGDB must be shifted to better accommodate a sequence-centric paradigm. In order to (1) show how the data at MaizeGDB relate to the maize genome, (2) relate MaizeGDB’s current sequence data with other sequence information as it becomes available, (3) become the keeper of maize’s ‘official’ set of gene models (which will enforce proper nomenclature), and (4) create a way to compare the various assemblies and annotations simultaneously, the feasibility of implementing of a genome browser at MaizeGDB was investigated and various available genome browser software were evaluated. Because the maize community communicates well, has a clear vision of their research problems, and has good ideas on how to best visualize a sequenced maize genome, we prepared a survey to gauge cooperators’ impressions of existing software and to find out what sorts of functionalities they would like to have in the MaizeGDB Genome Browser. Here we present the results of that survey as well as the rationale for why we chose GBrowse as MaizeGDB’s Genome Browser software, and the roadmap for implementation.