Article: Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides Journal: International Journal of Bioinformatics Research and Applications (IJBRA) 2005 Vol.1 No.4 pp.429 - 446 Abstract: 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<SUP align="right"><SMALL>K</SMALL></SUP> 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. Inderscience Publishers - linking academia, business and industry through research

Title: Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides

Authors: Osamu Maruyama, Akiko Matsuda, Satoru Kuhara

Addresses: Faculty of Mathematics, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812 8581, Japan. ' Graduate School of Systems Life Sciences, Kyushu University, Hakozaki 6 10 1, Higashi-ku, Fukuoka 812 8581, Japan. ' Graduate School of Genetic Resources Technology, Kyushu University, Hakozaki 6 10 1, Higashi-ku, Fukuoka 812 8581, Japan

Abstract: 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.

Keywords: phylogenetic trees; phylogenetic tree reconstruction; oligopeptide frequency; random sampling; bioinformatics; prokaryote genomes; microbial organisms; evolution.

DOI: 10.1504/IJBRA.2005.008446

International Journal of Bioinformatics Research and Applications, 2005 Vol.1 No.4, pp.429 - 446

Published online: 20 Dec 2005 *

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Title: Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides

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