Computer applications in the biosciences · 2005 · 36 citations · 8 references
Life SciencesBioinformaticsVisualizationComputational BiologyGenomicsSequence AnalysisPairwise AlignmentProfile Hidden Markov ModelsProtein Sequence AnalysisSequence AlignmentSequence Similarity SearchSequence VisualizationLogos ConstructionPairwise Alignment VisualizationProfile AlignmentProfile-sequence AlignmentProfile-to-sequence AlignmentProtein Family AnalysisProtein Profile ComparisonProtein Sequence Visualization
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.
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The Pfam Protein Families Database
Alex Bateman · Nucleic Acids Research · 2002 · 14.2K citations · Full text
The Pfam protein families database
Alex Bateman · Nucleic Acids Research · 2003 · 3.2K citations · Full text
Protein homology detection by HMM–HMM comparison
Johannes Söding · Bioinformatics · 2004 · 2.5K citations · Full text
Life Sciences, Bioinformatics, Protein Structure Prediction +16
HMM Logos for visualization of protein families
Benjamin Schuster‐Böckler, Jörg Schultz, Sven Rahmann · BMC Bioinformatics · 2004 · 233 citations · Full text