Visualizing profile-profile alignment: Pairwise HMM logos

Abstract

Summary: The availability of advanced profile-profile comparison tools, such as PRC or HHsearch demands sophisticated visualization 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. Two HMM logos, one for each profile, are drawn one upon the other. The aligned states are then highlighted and connected. © The Author 2005. Published by Oxford University Press. All rights reserved.