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Bioinformatics. 2005 Jun 15;21(12):2912-3. Epub 2005 Apr 12.

Visualizing profile-profile alignment: pairwise HMM logos.

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  • 1The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.


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.


A web interface offering online creation of pairwise HMM logos is available at Furthermore, software developers may download a Perl package that includes methods for creation of pairwise HMM logos locally.


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