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  1. Gramene
    Full Name of the Resource : A resource for comparative grass genomics
    Resource Category : Databases -> Plant Databases -> Plant- General plant databases

    Brief Description : Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses. 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 (http://www.gramene.org/japonica/mapview?chr=1) allows users to view the sequenced rice genome with sequenced features from multiple grass species aligned to it. BLAST (http://www.gramene.org/db/searches/blast) is a local alignment tool that allows users to find the best match to a sequence of interest. CMap (http://www.gramene.org/cmap/), a comparative mapping tool, allows users to view maps from different grass species and to construct comparisons between them. The Marker database (http://www.gramene.org/markers/) allows users to search for markers used for mapping in multiple grass species. The Protein database (http://www.gramene.org/protein/) allows users to find known rice proteins, learn about their functions, and find orthologs from other grasses. The Ontology database (http://www.gramene.org/plant_ontology/) allows users to search the standardized (controlled) vocabularies to find associated genes, proteins and phenotypes. The Mutant database (http://www.gramene.org/rice_mutant/) allows users to find rice genes with known phenotypes. The QTL database (http://www.gramene.org/qtl/) 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 (http://www.gramene.org/literature/) allows users to search Gramene's collection of curated citations. Future Plans:Future plans for Gramene include completing the migration to MySQL, the addition of a Diversity module, the addition of new maps and markers for millet in CMap, integration of the Plant Structure (anatomy) ontology from the Plant Ontology Consortium, the addition of phenotypes (QTL and mutants) and proteins from other grass species, updating of the existing data types, the addition of advanced search interfaces, off-site curation tools, and the furthering of outreach activities which will include the development of species specific educational pages and the organization of Research Coordination Network workshops. The Gramene project is a collaborative effort between Cold Spring Harbor Laboratory (http://www.cshl.edu/), the Department of Plant Breeding and Genetics at Cornell University (http://plbrgen.cals.cornell.edu/), and various national and international projects dedicated to cereal genomics and genetics research (see http://www.gramene.org/collaborators/). The database and the datasets are freely available for local use and installation. Quarterly releases provide researchers with current information and tools. For information about the most recent release, view the release notes at http://www.gramene.org/documentation/release_notes/ , and the database statistics at ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/statistics/. Gramene hosts the sequenced genome assembly of rice (Rice-japonica) and Arabidopsis provided by TIGR, in addition to the clone-based map of maize provided by AGI (http://www.genome.arizona.edu/fpc/maize/). Users may browse and search genes, markers, ESTs, cDNAs, clones, etc. on these genomes, as well as sequenced features from, sorghum, Triticeae (wheat, oat and barley), other grasses mapped on rice and maize genomes. See http://www.gramene.org/genome_browser/. The CMap Viewer can be used to search over 160 map sets (each with multiple maps of linkage groups or chromosomes) from 22 species, see http://www.gramene.org/cmap/. Over 4.5 million markers from more than 180 species can be searched to find a marker and get its detailed information on species, source and mapped locations, see http://www.gramene.org/markers/. The database contains over 68,000 protein entries detailing their biochemical characteristics and expression in association with the Gene (GO) and Plant (PO) Ontologies, sequence and cited literature, see http://www.gramene.org/protein/. The database contains about 1,400 genes from rice which have been characterized by phenotype. Among them, 425 genes have been fully annotated with phenotypic descriptions, associations to trait (TO), plant (PO) and gene ontologies (GO), map positions, alleles, phenotypic studies, germplasms, sequences, gene products, and related public references, see http://www.gramene.org/rice_mutant/. Over 9,800 QTL (http://www.gramene.org/qtl/) have been identified for numerous agronomic traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice. The Ontologies link (http://www.gramene.org/plant_ontology/) can be used to find keywords for plant structure, growth stages, traits, function, process, cellular component, environment and taxonomy. The Literature link (http://www.gramene.org/literature/) allows searching for articles about genes, proteins, QTL, markers, or ontologies. Sequence similarity matches can be done using the BLAST link (http://www.gramene.org/Multi/blastview). GrameneMart (http://www.gramene.org/Multi/martview) is a search tool that allows complex searches to filter out large amounts of superfluous data.

    Institute/s :
    Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724,USA
    Address of Institute/s :
    Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
    Country : United States

    Associated Institutes :

    • Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724USA
    • Department of Plant Breeding and Genetics, 240 Emerson Hall, USA
    • Institute for Genomic Diversity, USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY 14853, USA

    Associated Country : USA


    Authors/Contributors : Chengzhi Liang; Pankaj Jaiswal; Claire Hebbard; Shuly Avraham; Edward S. Buckler; Terry Casstevens; Bonnie Hurwitz; Susan McCouch; Junjian Ni; Anuradha Pujar; Dean Ravenscroft; Liya Ren; William Spooner; Isaak Tecle; Jim Thomason; Chih-wei Tung; Xuehong Wei; Immanuel Yap; Ken Youens-Clark; Doreen Ware; Lincoln Stein
    Contact Email : gramene@gramene.org, lstein@cshl.edu
    Year : 2008