Figure 4.

Sequence search on the E. coli K-12 MG1655 lexA (b4043) promoter region (125 bp upstream of the translation start point, shown in bold), using several of the search methods implemented in BioWord and a collection of known E. coli LexA-binding sites [[22]]. (Top left) Consensus logo representation of the LexA-binding site collection and its dyad motif. (Bottom left) Table format results for a Dyad Pattern search using with the dyad motif and 6-10 variable spacer. The overall Ri score is the sum of individual dyad scores. (Right) Table format results for a Gapped substring search using with CTGW and WCAG as substrings, maximum mismatch of 2 and 6-10 variable spacer. The overall score is the sum of dyad mismatch scores. (Bottom) Superimposed results for a pattern Search using the LexA-binding motif. In this output mode, the grey-scale shading intensity that highlights located sites is based on the information score (Ri), with darker shades indicating higher-scoring sites.

Anzaldi et al. BMC Bioinformatics 2012 13:124   doi:10.1186/1471-2105-13-124
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