RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes approximately 11,500 candidate binding sites for approximately 400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genome-wide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.
Novichkov
Pavel S
PS
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, State Scientific Center GosNIIGenetika, Moscow 117545, Russia.
Laikova
Olga N
ON
Novichkova
Elena S
ES
Gelfand
Mikhail S
MS
Arkin
Adam P
AP
Dubchak
Inna
I
Rodionov
Dmitry A
DA
D000465:Algorithms; D020816:Amino Acid Motifs; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D016680:Genome, Bacterial; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D009876:Operon; D016415:Sequence Alignment; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
D014157:Transcription Factors; D004247:DNA