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Nucleic Acids Research 2006 34(Database Issue):D358-D362; doi:10.1093/nar/gkj037
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Nucleic Acids Research, 2006, Vol. 34, Database issue D358-D362
© 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

ODB: a database of operons accumulating known operons across multiple genomes

Shujiro Okuda1,*, Toshiaki Katayama2, Shuichi Kawashima2, Susumu Goto1 and Minoru Kanehisa1,2

1Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan 2Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan

*To whom correspondence should be addressed. Tel: +81 774 38 3270; Fax: +81 774 38 3269; E-mail: okuda{at}kuicr.kyoto-u.ac.jp

Received August 15, 2005. Revised September 26, 2005. Accepted September 26, 2005.

Operon structures play an important role in co-regulation in prokaryotes. Although over 200 complete genome sequences are now available, databases providing genome-wide operon information have been limited to certain specific genomes. Thus, we have developed an ODB (Operon DataBase), which provides a data retrieval system of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The current version of our database contains about 2000 known operon information in more than 50 genomes and about 13 000 putative operons in more than 200 genomes. This system integrates four types of associations: genome context, gene co-expression obtained from microarray data, functional links in biological pathways and the conservation of gene order across the genomes. These associations are indicators of the genes that organize an operon, and the combination of these indicators allows us to predict more reliable operons. Furthermore, our system validates these predictions using known operon information obtained from the literature. This database integrates known literature-based information and genomic data. In addition, it provides an operon prediction tool, which make the system useful for both bioinformatics researchers and experimental biologists. Our database is accessible at http://odb.kuicr.kyoto-u.ac.jp/.


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