Document Detail

Identifying associations between amino acid changes and meta information in alignments.
MedLine Citation:
PMID:  21846738     Owner:  NLM     Status:  Publisher    
MOTIVATION: We present a method that identifies associations between amino acid changes in potentially significant sites in an alignment (taking into account several amino acid properties) with phenotypic data, through the phylogenetic mixed model. The latter accounts for the dependency of the observations (organisms). It is known from previous studies that the pathogenic aspect of many organisms may be associated with a single or just few changes in amino acids which have a strong structural and/or functional impact on the protein. Discovering these sites is a big step towards understanding pathogenicity. Our method is able to discover such sites in proteins responsible for the pathogenic character of a group of bacteria. RESULTS: We use our method to predict potentially significant sites in the RpoS protein from a set of 209 bacteria. Several sites with significant differences in biological relevant regions were found. AVAILABILITY: Our tool is publicly available on the web at CONTACT:
L Spangenberg; F Battke; M Graña; K Nieselt; H Naya
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2011-8-16
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  -     Publication Date:  2011 Aug 
Date Detail:
Created Date:  2011-8-17     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
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