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
Sui Yi et al., Genomic, regulatory and epigenetic mechanisms underlying duplicated gene evolution in the natural allotetraploid Oryza minuta Comparative and evolutionary genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-11
Licciardello Concetta et al., Characterization of the glutathione S-transferase gene family through ESTs and expression analyses within common and pigmented cultivars of Citrus sinensis (L.) Osbeck Genetics and crop biotechnology. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-39
Chen Bin et al., De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae). Parasites Vectors (2014) doi:10.1186/1756-3305-7-314
Chen Jia-Shing et al., Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues. BMC Research Notes (2014) doi:10.1186/1756-0500-7-15
Biselli Chiara et al., Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining Regular submissions. Rice (2014) doi:10.1186/1939-8433-7-1
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 USDAs 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.