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Nucleic Acids Research Advance Access published online on November 1, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp894
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

Pavel S. Novichkov1, Olga N. Laikova2, Elena S. Novichkova1, Mikhail S. Gelfand3,4, Adam P. Arkin1,5, Inna Dubchak1,6 and Dmitry A. Rodionov3,7,*

1Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2State Scientific Center GosNIIGenetika, Moscow 117545, 3Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, 4Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia, 5Department of Bioengineering, University of California, Berkeley, CA 94704-3224, 6Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 and 7Burnham Institute for Medical Research, La Jolla, CA 92037, USA

*To whom correspondence should be addressed. Tel: +1 858 646 3100; Fax: +1 858 795 5249; Email: rodionov{at}burnham.org

Received August 19, 2009. Revised September 29, 2009. Accepted October 5, 2009.

The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes ~11 500 candidate binding sites for ~400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genome-wide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.


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