A Resource for Comparative Grass Genomics

Release # 26

September 2007

News

Gramene Receives NSF Grant funding. See NSF Award announcement
Gramene uses Google Outreach Calendar
Sept 2007, V 26 release notes.
October 15-17, 2007 - 5th International Symposium of Rice Functional Genomics in Tsukuba, Japan
September/October Gramene Newsletter

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GENOMES: Browse assembled genomes for Oryza Sativa indica and japonica, Oryza rufipogon, Zea mays & Arabidopsis thaliana; Look for rice/maize synteny; Narrow your search with GrameneMart; Search for sequence alignment with BLAST; search by Gene Ontology.

PROTEINS: Search by PFam or ProSite or Browse by Gene Ontology using GO Slim.

COMPARATIVE MAPS: Browse genetic or physical maps for Wild Rice (Oryza sp. from OMAP), Rice, Maize, Wheat, Barley, Oats, Sorghum, and other grasses, or use the Comparative Map Viewer (CMap) to compare maps of different types and species. View map detail information

MARKERS: Search for Genetic markers (RFLPs, SSRs, etc.), DNA Probes (Primers, Overgos, etc.), Genomic Regions (Clones, FPContigs, etc.), and Sequences (GSSs, ESTs, etc.). Search by species such as Sorghum, by type such as SSR Primer Pair, or by species and type such as Rice SSR. Use the Simple Sequence Repeat Identification Tool (SSRIT).

TRAITS: Search the Genes or QTL database for important phenotype-releated loci such as Rice Genes, Rice QTL, Maize QTL. Don't forget to explore traits in Ontologies.

GENETIC DIVERSITY: Search for SNP and SSR allelic variation on loci of rice, maize, and wheat germplasms.

BIOCHEMICAL PATHWAYS: Search for a gene, protein, or pathway. Search for rice pathways associated with known reactions (exempli gratia starch biosynthesis) or get an overview of the metabolic network.

LITERATURE: Search the literature for your friends and topics of interest.

SPECIES PAGES provide overview information, pictures, and links to Gramene data for Oryza, Zea, Triticum, Hordeum, Avena, Setaria, Pennisetum, Secale, Sorghum, Zizania and Brachypodium.

SUBMISSION: Submit a Rice Gene or Ontology Term to Gramene, or ask a question.

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Visit with us at

Jan 12-16, 2008 PAG XVI Attend the Gramene Computer Demonstration and the Ontologies Workshop and computer demo. See our Posters!

Outreach Calendar
Presentation Materials

Gramene Tip:

Enter the Matrix to discover the best maps to compare to each other.

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Gramene is a curated, open-source, data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.

Last modified: Mon Nov 5 16:38:48 2007