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      Phylomat: an automated protein motif analysis tool for phylogenomics.

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          Abstract

          Recent progress in genomics, proteomics, and bioinformatics enables unprecedented opportunities to examine the evolutionary history of molecular, cellular, and developmental pathways through phylogenomics. Accordingly, we have developed a motif analysis tool for phylogenomics (Phylomat, http://alg.ncsa.uiuc.edu/pmat) that scans predicted proteome sets for proteins containing highly conserved amino acid motifs or domains for in silico analysis of the evolutionary history of these motifs/domains. Phylomat enables the user to download results as full protein or extracted motif/domain sequences from each protein. Tables containing the percent distribution of a motif/domain in organisms normalized to proteome size are displayed. Phylomat can also align the set of full protein or extracted motif/domain sequences and predict a neighbor-joining tree from relative sequence similarity. Together, Phylomat serves as a user-friendly data-mining tool for the phylogenomic analysis of conserved sequence motifs/domains in annotated proteomes from the three domains of life.

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          Author and article information

          Journal
          J. Proteome Res.
          Journal of proteome research
          1535-3893
          1535-3893
          : 3
          : 6
          Affiliations
          [1 ] University of Illinois, National Center for Supercomputing Applications, University of Illinois, Urbana, IL 61801, USA.
          Article
          10.1021/pr0499040
          15595740
          aa44ec78-4b4c-479e-bf4e-bd2cc1f90928
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