The problem of profile-profile comparison has a long history but has received a lot of attention recently.
This is a result of the growing number of well characterised protein families in databases such as Pfam. By adding additional information about properties of the entire family, it has been shown that profile-profile methods significantly increase sensitivity compared to profile-sequence comparison.
The availability of advanced profile-profile comparison tools such as PRC or HHsearch demand sophisticated visualisation tools not presently available. We introduce an approach built upon the concept of HMM Logos. The method illustrates the similarities of pairs of protein family profiles in an intuitive way.
We intended to construct pairwise HMM Logos to look as similar to HMM Logos as possible. This should facilitate their comprehension for users accustomed to HMM Logos. Therefore, we draw two HMM Logos, one for each aligned family. The overall height of the letter stacks represents the information content, the relative letter height corresponds to its emission probability. The Column width denotes the relative contribution, a combination of the expected number of emitted letters and the probability that the respective state is part of the family. Insert states are drawn in red. The aligned states in each HMM are framed and connected by a line. Omitted states are shaded in grey. The numbers above and below each Logo show state positions in the HMM.