Location: Corn Insects and Crop Genetics Research
Title: Genome Browser Survey Results and Browser Selection for MaizeGDB Authors
Submitted to: Cold Spring Harbor Meeting
Publication Type: Proceedings
Publication Acceptance Date: June 24, 2008
Publication Date: September 14, 2008
Citation: Sen, T.Z., Campbell, D.A., Schaeffer, M.L., Harper, E.C., Lawrence, C.J. 2008. Genome Browser Survey Results and Browser Selection for MaizeGDB. In: Genome Informatics Proceedings. Cold Spring Harbor Meeting Proceedings, Sept. 10-14, 2008, Hinxton, U.K. p. 1. Technical Abstract: Various platforms for genome browsing exist. Each has strengths and weaknesses, and users often champion their favorites (either based upon use needs or overall impressions). Faced with a need to shift MaizeGDB (http://www.maizegdb.org; the community database for maize genetics and genomics) towards a sequence-centric paradigm as a framework for the maize genome sequence (anticipated release by the end of 2008), we prepared a survey to find out what sorts of functionalities maize researchers most desire as well as to gauge researchers’ general impressions of existing software and sequence resources. Here we review the strengths and weaknesses of existing genome browser platforms, present the results of our survey, and review the rationale for choosing GBrowse to serve as MaizeGDB’s Genome Browser software. Our path to GBrowse implementation as well as a timeline for public release are also outlined.