Starting from the observation that a set of genes are co-regulated, one can suppose that some elements are shared by their upstream region, and one would like to detect such elements. A simple method to do so is search for position specific scoring matrix (PSSM) with a high information content. This method is implemented in info-gibbs.
The detection of PSSMs can be achieved with the program info-gibbs, which tries to find the PSSM with the maximal information content given the input sequences and a background model. As a study case, we will detect regulatory motifs in a set of the promoters of the bacteria Bacillus subtilis.