Figure 4From: SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statisticsExtension of shared trinucleotides, classifying of related promoter regions. The set SS1 corresponds to n promoter regions of a given bacterium sharing a pair of given trinucleotides t 1 and t 2. We compute the probabilities to obtain the encountered letters at the positions neighbouring t 1 and t 2, considering our n sequences. We retain the position associated with the letter which has the lowest probability to be obtained as soon as observed in this set of n sequences. We group sequences according to the letters at this position which have a low probability to be obtained (with at least eight related sequences). They constitute new sets of sequences to be evaluated with LRT statistical test (see Section "Computing a consensus motif and its statistical evaluation"). "INTERESTING SETS" means sets of promoter regions whose shared motif is over-represented in merged usptream sequences.Back to article page