Fig. 3

Algorithms for binding motif prediction based on TF-pentamer interaction energies. a In the Kmer-Sum algorithm, the IE score between a TF and a full-length DNA sequence is a summation of all the IE scores of the TF-pentamer complex (top part). After all IE scores between the TF and each permutation of the full-length DNA sequence are calculated, the binding motif is predicted based on the sequences with statistically significant IE scores among all possible sequences (lower part). b The PWM stacking algorithm generates a distribution of IE scores based on the sequence permutations for each pentamer of the original sequence. The PWM positions corresponding to the same position in the original structure are added together to form a PFM representing the TF’s TFBS, which is then converted to a PWM and binding motif logo