AgBase: Supporting functional modeling in agricultural organisms

Fiona M. McCarthy, Cathy R. Gresham, Teresia J. Buza, Philippe Chouvarine, Lakshmi R. Pillai, Ranjit Kumar, Seval Ozkan, Hui Wang, Prashanti Manda, Tony Arick, Susan M. Bridges, Shane C. Burgess

Research output: Contribution to journalArticlepeer-review

40 Scopus citations

Abstract

AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.

Original languageEnglish (US)
Pages (from-to)D497-D506
JournalNucleic acids research
Volume39
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 2011
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'AgBase: Supporting functional modeling in agricultural organisms'. Together they form a unique fingerprint.

Cite this