Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

• DOI: 10.1073/pnas.0913033107
• Publication Date: 2009-12-15T03:19:27Z
• Authors: Se-Ran Jun; Gregory E. Sims; Guohong A. Wu; Sung-Hou Kim
• Keywords: Feature (linguistics); Proteome; Low resolution

We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) whole proteomes. Features are l-mers amino acids, and each organism is represented profile frequencies all features. The selection length critical in the FFP method, we have developed procedure for identifying optimal lengths inferring prokaryotes, strictly speaking, proteome phylogeny. Our trees with proteomes 884 16 unicellular eukaryotes, 2 random sequences. To highlight branching order major groups, simplified tree monophyletic class or phylum branch support. In our (i) Archaea, Bacteria, Eukaryota, sequence outgroup clearly separated; (ii) Archaea Bacteria form sister group when rooted sequences; (iii) Planctomycetes, which possesses an intracellular membrane compartment, placed at basal position domain; (iv) almost groups most taxonomic levels, but many differences observed between built other methods; (v) previously "unclassified" genomes may be assigned to likely taxa. describe notable similarities those based on methods grouping prokaryotes.