A resource on rice and other grass genomes
Tutorial and training materials by OpenHelix
| Learn to use Gramene, a publicly available data resource for comparative genome analysis of grasses with genome browsers for many species, species information pages, various databases, an advanced search and more. Gramene contains genome browsers for Oryza sativa indica and japonica, O. glaberrima, O. rufipogon, Zea mays, Sorghum bicolor, Arabidopsis thaliana, Arabidopsis lyrata, Vitis vinifera and Populus trichocarpa. There are also tools to search for genetic markers, traits and biochemical pathways. Gramene's purpose is to provide added value to the many data sets available from public grass genomics studies and other projects.
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You'll learn:
- to perform effective searches and understand the genome browser displays
- to access advanced searches enabling multifaceted queries
- to access and use the various databases of markers, proteins, traits, gene diversity, and biochemical pathways
- to perform BLAST sequence searches of the genomes
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Related tutorialsThis tutorial is a part of the tutorial group Gramene-associated resources. You might find the other tutorials in the group interesting: | Recent BioMed Central research articles citing this resourceLiu Meiqin et al., Identification of stress-responsive genes in Ammopiptanthus mongolicus using ESTs generated from cold- and drought-stressed seedlings Plant-abiotic interactions. BMC Plant Biology (2013) doi:10.1186/1471-2229-13-88 Mishra Krishna Kumar et al., qDTY 12 1 : a locus with a consistent effect on grain yield under drought in rice Complex traits and quantitative genetics. BMC Genetics (2013) doi:10.1186/1471-2156-14-12 Suh Jung-Pil et al., Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice Regular submissions. Rice (2013) doi:10.1186/1939-8433-6-5 Wollbrett Julien et al., Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases Knowledge-based analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-126 Kwon Yong-Ik et al., DNA replication arrest leads to enhanced homologous recombination and cell death in meristems of rice OsRecQl4 mutants Genetics and crop biotechnology. BMC Plant Biology (2013) doi:10.1186/1471-2229-13-62 |
More about the resource:
Gramene is a collection of databases, tools and resources for research on various plant genomes. Some of the species included in this resource are rice, maize, Arabidopsis (a model organism for comparison), wheat, oats and several others. Some of the tools and databases included are a browser, an advanced search tool, and databases for markers, proteins, literature and more. The credit for Gramene goes to the Gramene team at both Cornell University and Cold Spring Harbor. Gramene was initially supported by the USDA’s CSREES program and since 2004 is supported by a grant from the National Science Foundation.
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