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Bioinformatics Advance Access originally published online on May 11, 2007
Bioinformatics 2007 23(14):1744-1752; doi:10.1093/bioinformatics/btm248
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/rcial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleotide composition string selection in HIV-1 subtyping using whole genomes

Xiaomeng Wu 1, Zhipeng Cai 1, Xiu-Feng Wan 2, Tin Hoang 1, Randy Goebel 1 and Guohui Lin 1,*

1Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada and 2Department of Microbiology, Miami University, Oxford, OH 45056, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The availability of the whole genomic sequences of HIV-1 viruses provides an excellent resource for studying the HIV-1 phylogenies using all the genetic materials. However, such huge volumes of data create computational challenges in both memory consumption and CPU usage.

Results: We propose the complete composition vector representation for an HIV-1 strain, and a string scoring method to extract the nucleotide composition strings that contain the richest evolutionary information for phylogenetic analysis. In this way, a large-scale whole genome phylogenetic analysis for thousands of strains can be done both efficiently and effectively. By using 42 carefully curated strains as references, we apply our method to subtype 1156 HIV-1 strains (10.5 million nucleotides in total), which include 825 pure subtype strains and 331 recombinants. Our results show that our nucleotide composition string selection scheme is computationally efficient, and is able to define both pure subtypes and recombinant forms for HIV-1 strains using the 5000 top ranked nucleotide strings.

Availability: The Java executable and the HIV-1 datasets are accessible through ‘http://www.cs.ualberta.ca/~ghlin/src/WebTools/hiv.php

Contact: ghlin{at}cs.ualberta.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Joaquin Dopazo

Received on November 11, 2006; revised on May 1, 2007; accepted on May 2, 2007

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