RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (D...

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Vydáno v:Nucleic acids research Ročník 40; číslo W1; s. W604 - W608
Hlavní autoři: Novichkov, P. S., Brettin, T. S., Novichkova, E. S., Dehal, P. S., Arkin, A. P., Dubchak, I., Rodionov, D. A.
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 01.07.2012
Témata:
Gene Expression Regulation, Bacterial
Gene Regulatory Networks
Genome, Bacterial
Genomics - methods
Internet
Nucleotide Motifs
Regulatory Sequences, Ribonucleic Acid
Regulon
Software
Transcription Factors - metabolism
Transcription, Genetic
User-Computer Interface
Web Services
ISSN:0305-1048, 1362-4962, 1362-4962
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Shrnutí:Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements.
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USDOE Office of Science (SC), Biological and Environmental Research (BER)
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gks562