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RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
Pavel S Novichkov1, Dmitry A Rodionov, Elena D Stavrovskaya
1Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. psnovichkov@lbl.org
Nucleic Acids Research
|June 15, 2010
Summary
RegPredict is a web server offering comparative genomics tools to reconstruct microbial regulons and regulatory motifs. It aids researchers in analyzing gene regulation across prokaryotic genomes efficiently.
Area of Science:
- Microbial genomics
- Systems biology
- Bioinformatics
Background:
- Microbial regulons are crucial for understanding gene regulation.
- Comparative genomics offers powerful tools for inferring regulatory networks.
Purpose of the Study:
- To develop and present the RegPredict web server for microbial regulon reconstruction and analysis.
- To provide tools for generating reference regulon sets and regulatory motif profiles across prokaryotic genomes.
Main Methods:
- Utilizes a comparative genomics approach for regulon reconstruction.
- Implements workflows for known regulatory motif analysis and *ab initio* novel regulon inference.
- Leverages genomic sequences, ortholog, and operon predictions from MicrobesOnline.
Main Results:
- Enables rapid generation of reference regulon sets and motif profiles.
- Introduces a novel concept of co-regulated orthologous operon clusters for distributed analysis.
- Provides a curated collection of regulatory motif position weight matrices.
Conclusions:
- RegPredict offers a comprehensive and interactive platform for microbial regulon analysis.
- The server facilitates efficient comparative analysis of large and multiple regulon clusters.
- It integrates diverse genomic and functional information for candidate regulon members.
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