A Resource for Comparative Grass Genomics
Release #29
March 2009
Release Notes
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Quick Start
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GENOMES:
Browse assembled genomes for
Oryza sativa indica
and japonica,
O. glaberrima,
O. rufipogon,
Zea mays,
Sorghum bicolor,
Arabidopsis thaliana,
Arabidopsis lyrata,
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.
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PROTEINS: Search by PFam or ProSite or Browse by Gene Ontology using GO Slim.
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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
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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 RFLP, or by species and type such as Rice
SSR. Use the Simple Sequence Repeat Identification Tool (SSRIT).
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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.
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GENETIC DIVERSITY:
Search for SNP and SSR allelic variation on loci of rice,
maize,
and wheat germplasms.
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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.
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LITERATURE: Search the literature for your friends and
topics of interest.
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SPECIES PAGES provide overview information, pictures, and links to Gramene data for Oryza,
Zea,
Triticum,
Hordeum,
Avena,
Setaria,
Pennisetum,
Secale,
Sorghum,
Zizania, and
Brachypodium.
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WEB SERVICES: Gramene
offers many useful web services like distributed annotation services (DAS)
for our genomes and genes, the GDPC for our diversity data, and semantic web
services for our QTLs.
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.
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Outreach Calendar
Presentation Materials
Gramene Tip:
The Marker database contains all map
sets, maps, and mappings, and should be considered to be the primary
source for information about maps and markers of various types.
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.
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