Figure 4From: Variable structure motifs for transcription factor binding sitesInformation content of gapped motifs. Examples showing how position dependencies induced by gap characters can affect the information content of motifs. Compare the gapped PWM C with the standard PWM D. Here the introduction of a gap has decreased the information content as the distribution over 7-mers is more vague. In contrast, PWM B has a higher information content than PWM D. Whether the gap is present or not, the bases around it remain Ts. Hence PWM B has a much sharper distribution over 7-mers. Note the difference in information content between gapped PWMs A and B. The reason is that A is very close to its own reverse complement whereas B is not. Hence A has a sharper distribution than B. All the information contents were calculated relative to a uniform 0-order Markov model.Back to article page