Figure 1

Example gapped PWM logo. An example to demonstrate the gapped PWM model and logo format: A gapped PWM, A, and 2 standard PWMs, B and C, are shown. All three define distributions over 5-mers: note that the last base of C is non-specific and not represented in the logo as it has no information content. The gapped PWM, A, can be viewed as a 70/30 mixture of B and C. That is, 70% of its binding sites look like sites from B and 30% look like sites from C. Put another way: 70% of its sites have a T/C inserted in the centre. The probability of the optional base being inserted in any given binding site is represented in 2 ways: firstly as a percentage written directly onto the logo; secondly, the base is also faded to represent how often it is present.