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PMID: 15608293 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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

Nucleic acids research ·Vol. 33 ·No. Database issue ·2005-01-01 ·Pages D98-102

González AD, Espinosa V, Vasconcelos AT, Pérez-Rueda E, Collado-Vides J

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 [email protected].

MeSH Terms

Base Sequence Binding Sites Databases, Nucleic Acid Gammaproteobacteria/genetics Gene Expression Regulation, Bacterial Genome, Bacterial Genomics Molecular Sequence Data Regulatory Sequences, Nucleic Acid Regulon Transcription Factors/metabolism

Chemicals

Transcription Factors

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

González Abel D

National Bioinformatics Center, Industria y San José, Capitolio Nacional, CP. 10200, Habana Vieja, Habana, Cuba.

Espinosa Vladimir

Vasconcelos Ana T

Pérez-Rueda Ernesto

Collado-Vides Julio

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gki054

Published

2005-01-01

Pages

D98-102

Language

English

Region

England

NLM ID

0411011

PMCID

PMC540008

Subset

Grants

NIGMS NIH HHS · GM62205 · United States

Databases

RefSeq

NC_000907, NC_000913, NC_002488, NC_002505, NC_002516, NC_002663, NC_002947, NC_003197, NC_003198, NC_003919, NC_004088, NC_004337, NC_004347, NC_004459, NC_004545, NC_004578, NC_004603

External Links

PubMed source DOI: 10.1093/nar/gki054 PMC Full Text View journal details

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

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