Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance

Author

Hao, Bailin ; Qi, Ji

Author_Institution

T-Life Res. Center, Fudan Univ., Shanghai, China

fYear

2003

fDate

11-14 Aug. 2003

Firstpage

375

Lastpage

384

Abstract

A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the appearance frequency of oligopeptides of a fixed length (up to K=6) in their proteomes. This is a method without fine adjustment and choice of genes. It can incorporate the effect of lateral gene transfer to some extent and leads to results comparable with the bacteriologists´ systematics as reflected in the latest 2001 edition of the Sergey´s manual of systematic bacteriology. A key point in our approach is subtraction of a random back-groundby using a Markovian model of order K-1 from the composition vectors to highlight the shaping role of natural selection.

Keywords

Markov processes; cellular biophysics; genetics; microorganisms; proteins; random sequences; Markovian model; avoidance signature; composition distance; genome data; lateral gene transfer; natural selection; oligopeptides; phylogenetic trees; prokaryote phylogeny; proteomes; random background; sequence alignment; Archaea; Bioinformatics; Frequency; Genomics; Microorganisms; Organisms; Phylogeny; Physics; Sequences; Systematics;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE

Print_ISBN

0-7695-2000-6

Type

conf

DOI

10.1109/CSB.2003.1227338

Filename

1227338