Phylomat: an automated protein motif analysis tool for phylogenomics.
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.
Graham
W Vallen
WV
University of Illinois, National Center for Supercomputing Applications, University of Illinois, Urbana, IL 61801, USA.
Tcheng
David K
DK
Shirk
Andrew L
AL
Attene-Ramos
Matias S
MS
Welge
Michael E
ME
Gaskins
H Rex
HR
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
D010446:Peptide Fragments; D011506:Proteins