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The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein LD1, Mungall C2, Shu S2, Caudy M3, Mangone M1, Day A1, Nickerson E1, Stajich J1,4, Harris TW1, Arva A1, and S Lewis2
2002. Genome Res.. 12(10): 1599-1610.
1 Cold Spring Harbor Laboratory, Cold Spring Harbor NY 11790, USA
2 Department of Molecular and Cell Biology, Berkeley Drosophila Genome Project, University of California, Berkeley CA 94720, USA
3 Department of Neuroscience, Cornell University Medical College at Burke Medical Research Institute, White Plains NY 10605, USA
4 University Program in Genetics, Duke University, Durham NC 27710, USA
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The Generic Model Organism System Database Project (GMOD) seeks to develop reuseable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations in order to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily-available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system web site.|, qq|GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.
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