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

被引：113

作者：

Novichkov, Pavel S. ^{[1
]}

Rodionov, Dmitry A. ^{[2
,3
]}

Stavrovskaya, Elena D. ^{[3
,4
]}

Novichkova, Elena S. ^{[1
]}

Kazakov, Alexey E. ^{[1
,3
]}

Gelfand, Mikhail S. ^{[3
,4
]}

Arkin, Adam P. ^{[1
,5
]}

Mironov, Andrey A. ^{[3
,4
]}

Dubchak, Inna ^{[1
,6
]}

机构：

[1] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA

[2] Burnham Inst Med Res, La Jolla, CA 92037 USA

[3] Russian Acad Sci, Inst Informat Transmiss Problems, Moscow 127994, Russia

[4] Moscow MV Lomonosov State Univ, Fac Bioengn & Bioinformat, Moscow 119992, Russia

[5] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94704 USA

[6] Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

基金：

美国国家科学基金会; 俄罗斯基础研究基金会;

关键词：

TRANSCRIPTIONAL REGULATORY NETWORKS; DATABASE; RECONSTRUCTION; PROTEOBACTERIA; PREDICTION; BACTERIA; SITES;

D O I：

10.1093/nar/gkq531

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：W299 / W307

页数：9

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