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.
You will learn:
This tutorial is a part of the tutorial group Model organisms. You might find the other tutorials in the group interesting:
TAIR: The Arabidopsis Information Resource
Saccharomyces Genome Database (SGD): Saccharomyces Genome Database
PhenomicDB: Phenotypes database
WormBase: Molecular and genetic information on Caenorhabditis elegans and related species
FlyBase: A resource for the genes, genome and molecular biology of Drosophila melanogaster and related species.
Mouse Genome Informatics (MGI): The Mouse Genome Informatics resource provides data, tools, and analyses for the mouse model organism.
Rat Genome Database (RGD): Rat Genome Database
ZFIN: The Zebrafish Information Network
This tutorial is a part of the tutorial group Plant resources. You might find the other tutorials in the group interesting:
Ensembl: Ensembl Genome Browser
TAIR: The Arabidopsis Information Resource
PlantGDB: Plant Genome Database
GBrowse: GBrowse User Introductory Tutorial
Ensembl Legacy: Older version of Ensembl Genome Browser
World Tour of Genomics Resources: A World Tour of Genome Resources for finding and learning the right resource for your needs.
Genome Databases (euk) : Genomic databases or repositories primarily aimed at eukaryotic organisms. Some may contain prokaryotic data as well.
Video Tip of the Week: Plant Reactome at Gramene: Reactome is one of our favorite tools to explore pathways. And they cover a wide range of species, which is helpful for many researchers. But there are times when having a topic-specific tool can be ev...
Tip of the Week: Plant comparative genomics using Plaza: Plaza, a resource for plant comparative genomics, has a lot more than meets the eye at first. Currently the database has comparative tools and data for nearly 2 dozen plants including monocots, dicots...
Genomics resource training scholarship, sponsored by Gramene and OpenHelix: Just thought our readers might like a heads up. I quote from a recent press release: Cold Spring Harbor Laboratory, Oregon State University and Cornell University, creators of the Gramene Resource for ...
Gramene Announces Scholarships for Groups Underrepresented in Science to Learn How to Use Bioinformatics and Genomics Resources: Cold Spring Harbor Laboratory, Oregon State University and Cornell University, creators of the Gramene Resource for Comparative Plant Genomics, partner with OpenHelix to offer online training on genomi...
DragonDB? Who knew....: Now, I like to immerse myself in databases--including some pretty obscure species. But even I had no idea there was a dragon database. Snapdragon! http://www.antirrhinum.net/ I'm working on an update...
Recent BioMed Central research articles citing this resource
Magwa Auma Risper et al., Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice ( Oryza sativa L.) Complex traits and quantitative genetics. BMC Genetics (2016) doi:10.1186/s12863-016-0340-2
Chien Chia-Hung et al., EXPath: a database of comparative expression analysis inferring metabolic pathways for plants Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Genomics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Genomics (2015) doi:10.1186/1471-2164-16-S2-S6
Ruengphayak Siriphat et al., Forward screening for seedling tolerance to Fe toxicity reveals a polymorphic mutation in ferric chelate reductase in rice. Rice (2015) doi:10.1186/s12284-014-0036-z
Chuang Trees-Juen et al., Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants. BMC Plant Biology (2015) doi:10.1186/s12870-015-0431-7
Oellrich Anika et al., An ontology approach to comparative phenomics in plants. Plant Methods (2015) doi:10.1186/s13007-015-0053-y