Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Comparative Genomics
            

GRAMENE: A TOOL FOR COMPARATIVE GRASS GENOMICS

¹ Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724

² Department of Plant Breeding, Cornell University, Ithaca NY 14853-1901

³ USDA-ARS Center for Agricultural Bioinformatics, 626 Rhodes Hall, Cornell Theory Center, Ithaca, NY 14853

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. It combines a semi-automatically generated database of cereal genomic and EST sequences, genetic maps, map relations and publications, with a curated database of rice mutants (genes and alleles), molecular markers and proteins. Genetic, physical and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize, sorghum, barley, wheat and oat are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using Gene Ontology (GO) terms which have been adopted by numerous model species databases. In this workshop, we present a brief overview of the two components of the database the rice genome browser, based upon a modified version of the Ensembl human genome browser developed by the EBI/Sanger, used to present cereal sequences in the framework of rice genomic clones and the comparative map viewer, Cmap, developed by Gramene, that combines sequence and name based correspondences for comparative displays of genetic and physical maps.