We generate the hexamer-specific experimental and theoretical PWMs with the DNA bindings of the hexamer sequences tested in the B1H dataset.
We use B1H results with affinity percentiles higher than 90%, 75% and 50%, for F2 and F3 domains, to generate the PWMs.
For each hexamer fragment of a finger domain, we select the binding site with highest affinity in the B1H experiment and assume that this is the 3bp specific binding of the hexamer.
The page will compare theoretical and experimental PWMs of the same hexamer sequence variant after selecting the finger domain, the binding trinucleotide, the structure used to calculate the theoretical PWM and the affinity percentile to calculate the experimental PWM.