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. 2005 Jan 1;33(Database issue):D98-102.
doi: 10.1093/nar/gki054.

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

Abel D González  1 , Vladimir Espinosa, Ana T Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides
Affiliations

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

Abel D González et al. Nucleic Acids Res. .

Abstract

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@cifn.unam.mx.

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Figures

Figure 1
Figure 1
TRACTOR_DB design. Main relationships between tables (oval arrows), and main queries performed by the interface program (stealth arrows).
See this image and copyright information in PMC

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