Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides
by Osamu Maruyama, Akiko Matsuda, Satoru Kuhara
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 1, No. 4, 2005

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.

Online publication date: Tue, 20-Dec-2005

The full text of this article is only available to individual subscribers or to users at subscribing institutions.

 
Existing subscribers:
Go to Inderscience Online Journals to access the Full Text of this article.

Pay per view:
If you are not a subscriber and you just want to read the full contents of this article, buy online access here.

Complimentary Subscribers, Editors or Members of the Editorial Board of the International Journal of Bioinformatics Research and Applications (IJBRA):
Login with your Inderscience username and password:

Username:        Password:          Forgotten your password?

Want to subscribe?
A subscription gives you complete access to all articles in the current issue, as well as to all articles in the previous three years (where applicable). See our Orders page to subscribe.

If you still need assistance, please email subs@inderscience.com