Information 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.
Reid et al. BMC Genomics 2010 11:30 doi:10.1186/1471-2164-11-30