Phylomat: An automated protein motif analysis tool for phylogenomics

W. Vallen Graham, David K. Tcheng, Andrew L. Shirk, Matias S. Attene-Ramos, Michael Welge, H Rex Gaskins

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)1289-1291
Number of pages3
JournalJournal of Proteome Research
Volume3
Issue number6
DOIs
StatePublished - Nov 1 2004

Keywords

  • Archaea
  • Bacteria
  • Domains
  • Eukarya
  • Evolution
  • Motifs
  • Phylogenomics
  • Proteome

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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