title: Phylomat: an automated protein motif analysis tool for phylogenomics.
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.
authors.affiliation: University of Illinois, National Center for Supercomputing Applications, University of Illinois, Urbana, IL 61801, USA.
authors.forename: W Vallen
authors.initials: WV
authors.lastname: Graham
authors.forename: David K
authors.initials: DK
authors.lastname: Tcheng
authors.forename: Andrew L
authors.initials: AL
authors.lastname: Shirk
authors.forename: Matias S
authors.initials: MS
authors.lastname: Attene-Ramos
authors.forename: Michael E
authors.initials: ME
authors.lastname: Welge
authors.forename: H Rex
authors.initials: HR
authors.lastname: Gaskins
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D019295:Computational Biology; D030562:Databases, Protein; D019143:Evolution, Molecular; D006801:Humans; D020407:Internet; D010446:Peptide Fragments; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D016415:Sequence Alignment
chemical_list: D010446:Peptide Fragments; D011506:Proteins