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. 2006 Jan 1;34(Database issue):D736-40.
doi: 10.1093/nar/gkj012.

OryGenesDB: a database for rice reverse genetics

G Droc  1 , M Ruiz, P Larmande, A Pereira, P Piffanelli, J B Morel, A Dievart, B Courtois, E Guiderdoni, C Périn
Affiliations

OryGenesDB: a database for rice reverse genetics

G Droc et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
Insertions within Os01g09550.1. Predicted gene Os01g09550.1, cDNA 001-037-H07 and Arabidopsis ortholog At4g29230.1 overlie flanking sequence data. Red, green and blue colors represent Tos17, T-DNA and Ac/Ds insertions, respectively. A contextual popup is open each time the mouse moves under a feature and links or feature-specific actions can be activated. See () for a tutorial and a more complete description. The text file containing the mapped sequences can be modified and is directly integrated in OryGenesDB using the GBrowse displaying third party tool. A list of clickable annotated landmarks is displayed and the mapping feature can be visualized as a glyph in the annotation layer (QUERY). See () for a tutorial and a more complete description.
See this image and copyright information in PMC

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