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Nucleic Acids Research 2005 33(Database Issue):D98-D102; doi:10.1093/nar/gki054
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Nucleic Acids Research, 2005, Vol. 33, Database issue D98-D102
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes

Abel D. González, Vladimir Espinosa, Ana T. Vasconcelos1, Ernesto Pérez-Rueda2 and Julio Collado-Vides3,*

National Bioinformatics Center, Industria y San José, Capitolio Nacional, CP. 10200, Habana Vieja, Habana, Cuba, 1 National Laboratory for Scientific Computing, Avenue Getulio Vargas 333, Quitandinha, CEP 25651-075, Petropolis, Rio de Janeiro, Brazil, 2 Depto. de Ingenierìa Celular y Biocatálisis, IBT-UNAM, Cuernavaca, Morelos, Mexico and 3 Center of Genomics, UNAM, AP 565-A Cuernavaca, CP. 62100, Morelos, Mexico

* To whom correspondence should be addressed. Tel: +527 773 132063; Fax: +527 773 175581; Email: collado{at}ccg.unam.mx

Received August 6, 2004; Revised and Accepted October 1, 2004

Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, transcription factors (TFs), TFs' binding sites and operons) within its genome. As more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcriptional regulation. In this work, we present TRACTOR_DB (TRAnscription FaCTORs' predicted binding sites in prokaryotic genomes), a relational database that contains computational predictions of new members of 74 regulons in 17 gamma-proteobacterial genomes. For these predictions we used a comparative genomics approach regarding which several proof-of-principle articles for large regulons have been published. TRACTOR_DB may be currently accessed at http://www.bioinfo.cu/Tractor_DB, http://www.tractor.lncc.br/ or at http://www.cifn.unam.mx/Computational_Genomics/tractorDB. Contact Email id is tractor{at}cifn.unam.mx.

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