Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Gramene: A Comparative Mapping Resource For The Grasses

Molly A Fogleman¹ , Immanuel Yap¹ , Doreen Ware² , Pankaj Jaiswal¹ , Junjian Ni¹ , Ken Y Clark² , Wei Zhao² , Liya Ren² , Kiran Ratnapu² , Steven Schmidt² , Lincoln Stein² , Susan R McCouch¹

¹  Department of Plant Breeding and Genetics, 240 Emerson Hall Cornell University Ithaca, NY 14853, USA

²  Cold Spring Harbor Laboratory, Bungtown Road Cold Spring Harbor, NY 11724, USA

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses, while using the rice genome as an anchor. Both automatic and manual curation are performed to combine and interrelate information on genomic and EST sequences, genetic, physical, and sequence-based maps, proteins, molecular markers, mutant phenotypes and QTL, and publications. There are currently nine main search modules within Gramene: Genome Browser, BLAST, CMap, Marker, Protein, Ontology, Mutant, QTL, and Literature. The Genome Browser allows users to view the sequenced rice genome with sequenced features from multiple grass species aligned to it. BLAST is a local alignment tool that allows users to find the best match to a sequence of interest. CMap, a comparative mapping tool, allows users to view maps from different grass species and to construct comparisons between them. The Marker database allows users to search for markers used for mapping in multiple grass species. The Protein database allows users to find known rice proteins, learn about their functions, and find orthologs from other grasses. The Ontology database allows users to search the standardized (controlled) vocabularies to find associated genes, proteins and phenotypes. The Mutant database allows users to find rice genes with known phenotypes. The QTL database allows users to find quantitative trait loci for multiple grass species such as rice, maize, oat, barley, pearl and foxtail millets and wild rice. The Literature database allows users to search Gramene's collection of curated citations.