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Virtual Footprint logo Version 3.0 Virtual Footprint logo

Short Introduction

Virtual Footprint is a new software suite for recognizing single or composite DNA patterns. It was especially designed to analyze transcription factor binding sites in whole bacterial genomes and their underlying regulatory networks. A pattern can consist of up to two subpatterns separated by a variable spacer region.
Virtual Footprint can deal with three types of subpatterns: Position Weight Matrices, IUPAC Code and Regular Expressions


There are two types of analyses available:

vfp_regulon Analysis of a whole prokaryotic genome with one regulator pattern
vfp_promoter Analysis of a promoter region with several regulator patterns

The most striking features:

  • Large library of bacterial position weight matrices derived from the PRODORIC database
  • Analysis of whole prokaryotic genomes and defintion of regulons
  • Visualization of genomic results in the interactive genome browser GBpro
  • Hyperlinks to the PRODORIC database
  • Phylogenetic footprinting of obtained matches (Regulog Analysis)

Please cite Virtual Footprint and results obtained by the use of Virtual Footprint as:

Münch, R., Hiller, K., Grote, A., Scheer, M., Klein, J., Schobert, M. & Jahn D. (2005)
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.
Bioinformatics 21, 4187-4189.

© 2003-2008 by Richard Münch •  Institute of Microbiology • Technical University of Braunschweig •  r.muench(at)