Virtual Footprint is a new sensitive search tool 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 various subpatterns separated by a variable spacer region, however this web version is restricted to bipartite patterns due to the time consuming calculation process. The definition of a subpattern is realized either by a position weigth matrix or a IUPAC consensus or a regular expression. A huge library of bacterial position weight matrices is provided.
Furthermore the programm offers the possibility of analzing the results according to their genomic context. Matches in coding regions can be excluded, the size of the upstream region (distance to the start codon) can be defined and the pattern orientation can be selected. The result is a list of potential binding sites and corresponding genes defining the whole regulon.
All matches are hyperlinked to an interactive genome browser to get a visialization of the genomic region and genes are linked to the PRODORIC database to provide further information about the molecular networks.