Literature DB >> 15827079

Visualizing profile-profile alignment: pairwise HMM logos.

Benjamin Schuster-Böckler1, Alex Bateman.   

Abstract

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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Year:  2005        PMID： 15827079     DOI： 10.1093/bioinformatics/bti434

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  24 in total

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3.  SCOOP: a simple method for identification of novel protein superfamily relationships.

Authors:  Alex Bateman; Robert D Finn
Journal:  Bioinformatics       Date:  2007-02-03       Impact factor: 6.937

4.  HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch.

Authors:  Mensur Dlakić
Journal:  Bioinformatics       Date:  2009-09-22       Impact factor: 6.937

Review 5.  Visualization of multiple alignments, phylogenies and gene family evolution.

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6.  Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferase.

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8.  webPRC: the Profile Comparer for alignment-based searching of public domain databases.

Authors:  Bernd W Brandt; Jaap Heringa
Journal:  Nucleic Acids Res       Date:  2009-05-06       Impact factor: 16.971

9.  Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes.

Authors:  Winona C Barker; Raja Mazumder; Sona Vasudevan; Jose-Luis Sagripanti; Cathy H Wu
Journal:  Virus Genes       Date:  2009-03-13       Impact factor: 2.332

10.  The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan.

Authors:  Gerard Manning; Susan L Young; W Todd Miller; Yufeng Zhai
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