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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| Vydané v: | Nucleic acids research Ročník 40; číslo W1; s. W604 - W608 |
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| Hlavní autori: | , , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
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England
Oxford University Press
01.07.2012
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| ISSN: | 0305-1048, 1362-4962, 1362-4962 |
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| Abstract | 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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| AbstractList | 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. 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.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. |
| Author | Dehal, P. S. Arkin, A. P. Dubchak, I. Brettin, T. S. Rodionov, D. A. Novichkov, P. S. Novichkova, E. S. |
| AuthorAffiliation | 1 Lawrence Berkeley National Laboratory, Berkeley, CA 94720, 2 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6420, USA, 3 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994 and 4 Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA |
| AuthorAffiliation_xml | – name: 1 Lawrence Berkeley National Laboratory, Berkeley, CA 94720, 2 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6420, USA, 3 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994 and 4 Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22700702$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1153747$$D View this record in Osti.gov |
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| Cites_doi | 10.1093/bioinformatics/bti321 10.1128/JB.00350-11 10.1093/nar/gkm910 10.1093/nar/gkq531 10.1093/nar/gkp894 10.1021/cr068309+ 10.1186/1471-2105-8-429 10.1038/nbt.1672 10.1128/JB.06412-11 10.1093/nar/gkr1014 10.1093/nar/gkp919 10.1074/jbc.M111.267963 10.1093/nar/gkm994 |
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| SubjectTerms | 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 |
| Title | RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics |
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