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UNLABELLED: 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@sanger.ac.uk.

Original publication

DOI

10.1093/bioinformatics/bti434

Type

Journal article

Journal

Bioinformatics (Oxford, England)

Publication Date

06/2005

Volume

21

Pages

2912 - 2913

Addresses

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. bsb@sanger.ac.uk

Keywords

Proteins, Markov Chains, Gene Expression Profiling, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Models, Chemical, Models, Molecular, Computer Graphics, Computer Simulation, User-Computer Interface