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Nucleic Acids Research Advance Access originally published online on November 16, 2006
Nucleic Acids Research 2007 35(Database issue):D407-D412; doi:10.1093/nar/gkl865
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Nucleic Acids Research, 2007, Vol. 35, Database issue D407-D412
© 2006 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.

Articles

RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

Alexei E. Kazakov1, Michael J. Cipriano2, Pavel S. Novichkov3, Simon Minovitsky2, Dmitry V. Vinogradov1, Adam Arkin2,4,5,6, Andrey A. Mironov1,7,8, Mikhail S. Gelfand1,7,8,* and Inna Dubchak2,9,*

1 Institute for Information Transmission Problems, RAS. Bolshoi Karetny pereulok 19 Moscow, 127994, Russia 2 Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, CA 94720, USA 3 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA 4 Howard Hughes Medical Institute 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA 5 Department of Bioengineering, University of California Berkeley, CA, 94710, USA 6 Virtual Institute of Microbial Stress and Survival, Berkeley CA, 94710, USA 7 Faculty of Bioengineering and Bioinformatics, Moscow State University Vorobievy Gory 1-73, Moscow 119992, Russia 8 State Research Center GosNIIGenetika. 1-j Dorozhny proezd 1 Moscow, 117545, Russia 9 Department of Energy Joint Genome Institute 2800 Mitchell Drive,Walnut Creek, CA 94598, USA

*To whom correspondence should be addressed. Tel: +1 510 495 2419; Fax: +1 510 486 5614; Email: ildubchak{at}Ibl.gov

Received August 14, 2006. Revised September 19, 2006. Accepted October 4, 2006.

RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms Escherichia coli and Bacillus subtilis or are entirely computationally derived. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains the following types of experimental data: the activation or repression of transcription by an identified direct regulator, determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA), mapping or prediction of a binding site for a regulatory protein and characterization of regulatory mutations. Currently, RegTransBase content is derived from about 3000 relevant articles describing over 7000 experiments in relation to 128 microbes. It contains data on the regulation of about 7500 genes and evidence for 6500 interactions with 650 regulators. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species. RegTransBase is available at http://regtransbase.lbl.gov.

*Correspondence may also be addressed to Mikhail S. Gelfand. Tel: +7 916 609 2971; Fax: +7 495 209 0579; Email: gelfand{at}iitp.ru


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