Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.
CONCLUSIONS
A new online framework for the accurate and integrative prediction of transcription factor binding sites (TFBSs) in prokaryotes was developed. The system consists of three interconnected modules: (1) The PRODORIC database as a comprehensive data source and extensive collection of TFBSs with corresponding position weight matrices. (2) The pattern matching tool Virtual Footprint for the prediction of genome based regulons and for the analysis of individual promoter regions. (3) The interactive genome browser GBPro for the visualization of TFBS search results in their genomic context and links to gene and regulator-specific information in PRODORIC. The aim of this service is to provide researchers a free and easy to use collection of interconnected tools in the field of molecular microbiology, infection and systems biology.


BACKGROUND
http://www.prodoric.de/vfp.
Münch
Richard
R
Institute of Microbiology, Technical University Braunschweig, Germany.
Hiller
Karsten
K
Grote
Andreas
A
Scheer
Maurice
M
Klein
Johannes
J
Schobert
Max
M
Jahn
Dieter
D
D000465:Algorithms; D001426:Bacterial Proteins; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D030562:Databases, Protein; D005798:Genes, Bacterial; D016678:Genome; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D016247:Information Storage and Retrieval; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D020218:Response Elements; D012680:Sensitivity and Specificity; D012984:Software; D014157:Transcription Factors / Q000235:genetics; D014584:User-Computer Interface
D001426:Bacterial Proteins; D014157:Transcription Factors