Biological system and scheme of the strategy. a) The two component system VirR/VirS and its experimentally validated targets are here schematically represented. Information mainly come from studies performed in Str. 13; modified from . b) Scheme illustrating the two step strategy that allowed to use information coming mainly from a single strain to do the predictions on all other strains in a less biased way. In the first step a position weight matrix (PWM) calculated from a limited number of experimentally validated motifs is used to scan the genomes and to make a list of possible targets. Within that list we looked for sequences corresponding to known targets using clustering, we retrieved their motifs and we obtained a second PWM. This includes the variability of the motif in several strains and was used for the final scan of the genomes.