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 language | English (US) |
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Pages (from-to) | 1289-1291 |
Number of pages | 3 |
Journal | Journal of Proteome Research |
Volume | 3 |
Issue number | 6 |
DOIs | |
State | Published - Nov 1 2004 |
Keywords
- Archaea
- Bacteria
- Domains
- Eukarya
- Evolution
- Motifs
- Phylogenomics
- Proteome
ASJC Scopus subject areas
- Biochemistry
- Chemistry(all)