RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

Journal Article · Wed May 26 04:00:00 EDT 2010 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkq531· OSTI ID:986246

Novichkov, Pavel S; Rodionov, Dmitry A; Stavrovskaya, Elena D; Novichkova, Elena S; Kazakov, Alexey E; Gelfand, Mikhail S; Arkin, Adam P; Mironov, Andrey A; Dubchak, Inna

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.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Genomics Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 986246
• Report Number(s): LBNL-3805E
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 38; ISSN 03051048
• Country of Publication: United States
• Language: English

Related Subjects

60 APPLIED LIFE SCIENCES
FUNCTIONALS
GENES
MATRICES