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
Ta N. K. et al., Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice. EvoDevo (2017) doi:10.1186/s13227-017-0065-y
Chopra Ratan et al., Genome-wide association analysis of seedling traits in diverse Sorghum germplasm under thermal stress. BMC Plant Biology (2017) doi:10.1186/s12870-016-0966-2
Ereful C. Nelzo et al., Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs. Rice (2016) doi:10.1186/s12284-016-0123-4
Li Lingli et al., Comparative transcriptome sequencing and de novo analysis of Vaccinium corymbosum during fruit and color development Genomics and evolution. BMC Plant Biology (2016) doi:10.1186/s12870-016-0866-5
Chen Likai et al., High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. Rice (2016) doi:10.1186/s12284-016-0121-6