title: RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
abstract: RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. psnovichkov@lbl.org
authors.forename: Pavel S
authors.initials: PS
authors.lastname: Novichkov
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
authors.forename: Elena D
authors.initials: ED
authors.lastname: Stavrovskaya
authors.forename: Elena S
authors.initials: ES
authors.lastname: Novichkova
authors.forename: Alexey E
authors.initials: AE
authors.lastname: Kazakov
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Mironov
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
mesh_terms: D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D009876:Operon; D018085:Regulon; D012984:Software; D040141:Staphylococcaceae / Q000235:genetics; D018511:Systems Integration; D014584:User-Computer Interface