Fig. 1.

A comparison between PWM score and binding site strength in the D. melanogaster even-skipped stripe 1 enhancer. The even-skipped stripe 1 enhancer on chromosome 2R is dense with binding sites. We compare the raw PWM scores (circles) and the λ-scaled binding strength (height of the bars) for each of these binding sites, colour-coded by the type of TF. Based on raw PWM scores, one might assume that the Caudal site indicated by the first blue arrow would have a lower binding strength than the Kruppel site indicated by the second blue arrow; Eq. 3 instead of Eq. 5, it becomes evident that the opposite is the more likely scenario. The third arrow points to a location where a Kruppel and a Bicoid binding site overlap. Here, the λ adjusted binding strength estimates would suggest that Bicoid binding site is stronger, while a raw PWM score would suggest the opposite. These results illustrate how using raw PWM scores may result in biased interpretation of the relative binding strength of TFs