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Flow chart for per-finger prediction of PWMs. The ability of every individual zinc finger domain (as predicted by HMMER (32)) to bind all possible 4 bp DNA sequences is scored; here we show a pre-trained SVM that used the seven-contact model. The SVM scores for all possible 256 DNA variants are subsequently used to compute the final PWM using equation (3). Finally, the PWM is visualized in the form of a sequence logo.
