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Bioinformatics Advance Access originally published online on April 12, 2005
Bioinformatics 2005 21(12):2912-2913; doi:10.1093/bioinformatics/bti434
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Visualizing profile–profile alignment: pairwise HMM logos

Benjamin Schuster-Böckler * and Alex Bateman

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

*To whom correspondence should be addressed.

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.

Availability: A web interface offering online creation of pairwise HMM logos is available at http://www.sanger.ac.uk/Software/analysis/logomat-p. Furthermore, software developers may download a Perl package that includes methods for creation of pairwise HMM logos locally.

Contact: bsb{at}sanger.ac.uk


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