Figure 7.

Using promoter cis-features to annotate regulatory regions. We recognized different PhoP binding box orientations and patterns, and RNA polymerase close class II and medium class I sites, and isolated the corresponding regions of promoters with similar features. Then, we described the similarity among DNA sequences in terms of the entropy of the frequency of the dominant base. This allowed us to visualize the variability of the promoter DNA sequences in terms of useful information (low values). These alignments with maximum information content could not be identified without using distinct cis-features harboring different patterns. This is clearly shown when the plain alignment of the intergenic region of all 11 promoters is performed (not shown).