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:

  • 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 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

Roy Somnath et al., Genetic diversity and structure in hill rice ( Oryza sativa L.) landraces from the North-Eastern Himalayas of India Plant population genetics. BMC Genetics (2016) doi:10.1186/s12863-016-0414-1

Segami Shuhei et al., Detection of Novel QTLs Regulating Grain Size in Extra-Large Grain Rice ( Oryza sativa L.) Lines. Rice (2016) doi:10.1186/s12284-016-0109-2

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

Yang Shuai-Qi et al., REL2 , A Gene Encoding An Unknown Function Protein which Contains DUF630 and DUF632 Domains Controls Leaf Rolling in Rice. Rice (2016) doi:10.1186/s12284-016-0105-6

Zhang Hong-Wei et al., Dissection of the qTGW1.1 region into two tightly-linked minor QTLs having stable effects for grain weight in rice Complex traits and quantitative genetics. BMC Genetics (2016) doi:10.1186/s12863-016-0410-5