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Figure 4 | BMC Bioinformatics

Figure 4

From: SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

Figure 4

Extension 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.

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