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Nucleic Acids Research Advance Access originally published online on November 26, 2008
Nucleic Acids Research 2009 37(Database issue):D992-D995; doi:10.1093/nar/gkn821
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Nucleic Acids Research, 2009, Vol. 37, Database issue D992-D995
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

OryGenesDB 2008 update: database interoperability for functional genomics of rice

Gaëtan Droc, Christophe Périn, Sébastien Fromentin and Pierre Larmande*

CIRAD Dept BIOS UMR DAP - TA40/03 34398 Montpellier France

*To whom correspondence should be addressed. Tel: +33 4 67 61 54 45; Fax: +33 4 67 61 56 05; Email: pierre.larmande{at}cirad.fr

Received September 15, 2008. Revised October 10, 2008. Accepted October 13, 2008.

OryGenesDB (http://orygenesdb.cirad.fr/index.html) is a database developed for rice reverse genetics. OryGenesDB contains FSTs (flanking sequence tags) of various mutagens and functional genomics data, collected from both international insertion collections and the literature. The current release of OryGenesDB contains 171 000 FSTs, and annotations divided among 10 specific categories, totaling 78 annotation layers. Several additional tools have been added to the main interface; these tools enable the user to retrieve FSTs and design probes to analyze insertion lines. The major innovation of OryGenesDB 2008, besides updating the data and tools, is a new tool, Orylink, which was developed to speed up rice functional genomics by taking advantage of the resources developed in two related databases, Oryza Tag Line and GreenPhylDB. Orylink was designed to field complex queries across these three databases and store both the queries and their results in an intuitive manner. Orylink offers a simple and powerful virtual workbench for functional genomics. Alternatively, the Web services developed for Orylink can be used independently of its Web interface, increasing the interoperability between these different bioinformatics applications.


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