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 resourceKong Lei et al., ABrowse - a customizable next-generation genome browser framework. BMC Bioinformatics (2012) doi:10.1186/1471-2105-13-2 Joshi Trupti et al., Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics Selected articles from the Tenth Asia Pacific Bioinformatics Conference (APBC 2012) The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). BMC Genomics (2012) doi:10.1186/1471-2164-13-S1-S15 Kalavacharla Venu et al., Identification and analysis of common bean ( Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biology (2011) doi:10.1186/1471-2229-11-135 Luo Hongmei et al., Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers The 2010 International Conference on Bioinformatics and Computational Biology (BIOCOMP 2010): Genomics BIOCOMP 2010. The 2010 International Conference on Bioinformatics and Computational Biology. BMC Genomics (2011) doi:10.1186/1471-2164-12-S5-S5 Wang Jun et al., Rice-Map: a new-generation rice genome browser. BMC Genomics (2011) doi:10.1186/1471-2164-12-165 |
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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