OryGenesDB: a database for rice reverse genetics

G. Droc, M. Ruiz, P. Larmande, A.B. Pereira, P. Piffanelli, J.B. Morel, A. Dievart, B. Courtois, E. Guiderdoni, C. Perin

    Research output: Contribution to journalArticleAcademicpeer-review

    57 Citations (Scopus)

    Abstract

    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.
    Original languageEnglish
    Pages (from-to)D736-D740
    JournalNucleic acids research
    Volume34
    DOIs
    Publication statusPublished - 2006

    Keywords

    • functional genomics
    • annotation
    • resources

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  • Cite this

    Droc, G., Ruiz, M., Larmande, P., Pereira, A. B., Piffanelli, P., Morel, J. B., ... Perin, C. (2006). OryGenesDB: a database for rice reverse genetics. Nucleic acids research, 34, D736-D740. https://doi.org/10.1093/nar/gkj012