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.|
- 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
This tutorial is a part of the tutorial group Gramene-associated resources. You might find the other tutorials in the group interesting:
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Recent BioMed Central research articles citing this resource
Zimmer D Andreas et al., Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions Plant genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-498
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
Megraw Molly et al., Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biology (2013) doi:10.1186/gb-2013-14-8-r85
Saithong Treenut et al., Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration Empirical systems biology. BMC Systems Biology (2013) doi:10.1186/1752-0509-7-75
Meskauskiene Rasa et al., Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. Plant Methods (2013) doi:10.1186/1746-4811-9-33
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.
The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.