OryGenesDB 2008 update: Database interoperability for functional genomics of rice

Droc Gaëtan, Perin Christophe, Fromentin Sébastien, Larmande Pierre. 2009. OryGenesDB 2008 update: Database interoperability for functional genomics of rice. Nucleic Acids Research, 37, suppl. 1, D992-D995

https://doi.org/10.1093/nar/gkn821

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Quartile : Q1, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY

Résumé : 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.

Mots-clés Agrovoc : Oryza, banque de gènes, génie génétique, système d'information, séquence nucléotidique, adn, pool de gènes, génome, mutant

Mots-clés complémentaires : Gène d'intérêt, Réversion

Classification Agris : F30 - Génétique et amélioration des plantes
C30 - Documentation et information

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

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