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


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


BACKGROUND
Supplementary data are available at Bioinformatics online.
Wu
Xiaomeng
X
Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada.
Cai
Zhipeng
Z
Wan
Xiu-Feng
XF
Hoang
Tin
T
Goebel
Randy
R
Lin
Guohui
G
D001482:Base Composition; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D005821:Genetic Techniques; D005822:Genetic Vectors; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D015497:HIV-1 / Q000235:genetics*; D015233:Models, Statistical; D009711:Nucleotides / Q000737:chemistry; D010802:Phylogeny; D012313:RNA / Q000235:genetics; D011995:Recombination, Genetic; D015203:Reproducibility of Results
D009711:Nucleotides; D012313:RNA