Figure 2

Sub-HMM Extraction Process. An example of the sub-HMM excision process is given for the fatty acid desaturase domain (PF00487). The light gray line is the KL-divergence of each position in the original HMM. The darker line is the result of smoothing with s = 8. The horizontal line is the threshold, set to the average KL-divergence. Each section of the curve with more than l = 8 positions above the threshold produces a sub-HMM. The details about the different parameters are given in the Method section.