1. Gramene Objectives Provide researchers working on grasses and plants in general with a bird’s eye view of the grass genomes and their organization. Work with the community to provide passport information on maps (genetic and physical), markers, sequences, genes, gene products, mutants, QTL and literature of the major grass crops. Develop controlled vocabularies (ontologies) in collaboration with the Gene Ontology and Plant Ontology consortia to describe gene/phenotype’s functional characterization and expression profile. Develop a database and tools to store, visualize and analyze data on genetics, genomics, proteomics, and biochemistry of grass plants. Develop bioinformatic community resources for discovery in plants. Maps -Genetic -Physical -Sequence -QTL -Deletion Genome Browser -Rice Genome -Genetic markers -Gene Models -Proteins -Full length cDNAs -ESTs and Clusters -GSS and Clusters -BACs and BAC ends -Repeats Species Rice, Wild rice, Maize, Wheat Barley, Oat Sorghum, Sugarcane Rice Genome Proteins Mutants QTLs Literature Ontologies Gene Ontology Plant Ontology Trait Ontology Gramene Datasets CMap Comparative map displays, Map feature search gramene.org/cmap/ Genome Browser Dynamic display of assembled rice genome and aligned sequence (mapped) features gramene.org/japonica/mapview? BLAST Pairwise sequence alignment of Gramene data sets gramene.org/db/searches/blast Protein Search proteins from rice gramene.org/protein/ Mutant Search phenotypic variants gramene.org/rice_mutant QTL Search quantitative trait loci gramene.org/qtl/ Ontologies A resource for standardized glossaries gramene.org/plant_ontology/ Literature Search Gramene’s collection of curated citations gramene.org/literature Resources Useful links gramene.org/resources Tutorials How to use Gramene? gramene.org/workshop_tutorial.html Site map Gramene database links gramene.org/sitemap.html FTP Download Download the entire database and datasets under Open Source ftp://ftp.gramene.org/pub/gramene/ Mailing ListJoin our mailing list gramene.org/mailarch/ Gramene project is a collaboration between the Cold Spring Harbor lab, NY and the Cornell University, NY, USA. It is supported by an IFAFS grant from the USDA Cooperative State Research and Education Service (CSREES), PGI grant from the National Science Foundation and a cooperative agreement through the USDA Agricultural Research Service. © Gramene database 2004 Useful Gramene sites A Comparative mapping resource GRAMENE A Bird’s Eye View of Grass Genomes Web site www.gramene.org Contact gramene@gramene.org

2. View the sequenced rice genome with features from multiple grass species aligned to the Genome Browser. Allows views of 2 megabases to 10 basepairs. Features support linking to internal pages and external reference resources. Find known rice proteins and learn about their functions. Provides external links to GenBank and SwissProt as well as internal links to the Ontology database and the Genome Browser. Search the Gramene database. Find rice genes with known phenotypes, such as this semidwarf-1 gene. Provides links to their mapped position in CMap. View maps from different grass species and construct comparisons between them. Find quantitative trait loci for multiple grass species. Provides links to their mapped position in CMap. Use the “Feedback” button for questions, suggestions and difficulties. We would like to hear from you. A collection of useful links, including genomic projects, other grass databases and bioinformatic resources. www.gramene.org Useful Gramene website links, including links for Tutorials and Downloads. If you are new to our site, we suggest you review our tutorials before starting.