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Bioinformatics Advance Access published online on August 18, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti635
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 11, 2005
Revised August 15, 2005
Accepted August 15, 2005

Applications note

Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes

Richard Münch 1, Karsten Hiller 1, Andreas Grote 2, Maurice Scheer 3, Johannes Klein 1, Max Schobert 1, and Dieter Jahn 1*

1 Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
2 Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany; Institute of Biochemical Engineering, Technical University Braunschweig, Gaußstrasse 17, 38106 Braunschweig, Germany
3 Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany; Department of Informatics, University of Applied Sciences Wolfenbüttel, Am Exer 2, 38302 Wolfenbüttel, Germany

* To whom correspondence should be addressed.
Dieter Jahn, E-mail: d.jahn{at}tu-bs.de


  Abstract

Summary: 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 (PWMs). 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.

Availability: http://www.prodoric.de/vfp.


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