Prokaryote Phylogeny without Sequence Alignment: From Avoidance Signature to Composition Distance

Authors:
Bailin Hao;Ji Qi
Affiliations:
-;-
Venue:
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Year:
2003

Citing 0
Cited 2

Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method

International Journal of Bioinformatics Research and Applications
An ant colony optimisation algorithm for constructing phylogenetic tree

International Journal of Computer Applications in Technology

Quantified Score

Hi-index	0.00

Visualization

Abstract

A new and essentially simple method to reconstructprokaryotic phylogenetic trees from their complete genomedata without using sequence alignment is proposed. It isbased on the appearance frequency of oligopeptides of afixed length (up to K = 6) in their proteomes.This isa method without fine adjustment and choice of genes. Itcan incorporate the effect of lateral gene transfer to someextent and leads to results comparable with the bacteriologists'systematics as reflected in the latest 2001 edition ofthe Bergey's Manual of Systematic Bacteriology [1, 2]. Akey point in our approach is subtraction of a random backgroundby using a Markovian model of order K - 1 from thecomposition vectors to highlight the shaping role of naturalselection.