A Resource for Comparative Grass Genomics

Release # 27

April 2008

News

iPlant collaborative open letter of invitation to the plant biology community
Workshop on Cereal Genomics, Cold Spring Harbor, October 14-20,2008
Gramene Receives NSF Grant funding. See NSF Award announcement
Gramene uses Google Outreach Calendar

Have Questions...?

Quick Search Help
OpenHelix Tutorial and Exercises (coming soon), as well as older Archived Tutorials, V26 - See what you can do and how to do it.
Ask questions through Feedback or Email.
See FAQ.

Quick Start

GENOMES: Browse assembled genomes for Oryza sativa indica and japonica, O. glaberrima, O. rufipogon, Zea mays, Sorghum bicolor, Arabidopsis thaliana, Vitis vinifera, and Populus trichocarpa. 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 (e.g., 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.

Note! Although we continually work to make Gramene compatible with all browsers, if you're having difficulty viewing Gramene, try using a different browser. Please report any problems with browsers through Gramene Feedback.

Visit with us at

Outreach Calendar
Presentation Materials

Gramene Tip:

The QTL Power Search can help to make your searches more exact. For example, if searching for linkage group 1* in the QTL simple search, results would include linkage groups 11 and 12 as well. With the Power Search, users are able to exclude 11 and/or 12.

Browse All Tips

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: Wed May 14 10:11:33 2008