Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides.

In this paper, we propose a method for reconstructing phylogenetic trees of a given set of prokaryote organisms by randomly sampling relatively small oligopeptides of a fixed length from their complete proteomes. For each of the organisms, a vector of frequencies of the sampled oligopeptides is generated and used as a building block in reconstructing phylogenetic trees. By this procedure, multiple phylogenetic trees are created independently, and a consensus tree of those trees is created. We have applied our method to a set of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, using around 10% of all the 3,200,000 oligopeptides of length 5 in a reconstruction of a single phylogenetic tree. Our consensus tree agrees with the tree of Bergey's Manual in most of the basic taxa. In addition, they have almost the same quality as the trees of the same organisms reconstructed using all the 20^{K oligopeptides of length K = 5 and 6 given by Qi et al. Thus we can conclude that, the frequencies of a relatively small number of oligopeptides of length 5, even if those oligopeptides are determined in a random method, has phylogenetic information almost equivalent to the frequencies of all the oligopeptides of length 5 or 6.}