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Nucleic Acids Research 2006 34(Database Issue):D736-D740; doi:10.1093/nar/gkj012
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Nucleic Acids Research, 2006, Vol. 34, Database issue D736-D740
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

OryGenesDB: a database for rice reverse genetics

G. Droc, M. Ruiz, P. Larmande, A. Pereira1, P. Piffanelli, J. B. Morel2, A. Dievart, B. Courtois, E. Guiderdoni and C. Périn*

CIRAD, UMR PIA 1096 TA 40/03 Avenue Agropolis 34398 Montpellier Cedex 5, France 1Wageningen UR, Plant Research International PO Box 16, 6700 AA, Wageningen, The Netherlands 2CIRAD/INRA UMR BGPI TA 41/K Campus International de Baillarguet 34398 Montpellier Cedex 05, France

*To whom correspondence should be addressed at TA40/03 Avenue Agropolis, 34398 Montpellier Cedex 5, France. Tel: +33 4 67 61 71 85; Email: perin{at}cirad.fr

Received June 9, 2005. Revised September 12, 2005. Accepted September 12, 2005.

Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (http://orygenesdb.cirad.fr/), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an ‘anchoring’ option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.


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