Whole genome composition distance for HIV-1 genotyping.
Existing HIV-1 genotyping systems require a computationally expensive phase of multiple sequence alignments and the alignments must have a sufficiently high quality for accurate genotyping. This is particularly a challenge when the number of strains is large. Here we propose a whole genome composition distance (WGCD) to measure the evolutionary closeness between two HIV-1 whole genomic RNA sequences, and use that measure to develop an HIV-1 genotyping system. Such a WGCD-based genotyping system avoids multiple sequence alignments and does not require any pre-knowledge about the evolutionary rates. Experimental results showed that the system is able to correctly identify the known subtypes, sub-subtypes, and individual circulating recombinant forms.
Wu
Xiaomeng
X
Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada.
Goebel
Randy
R
Wan
Xiu-Feng
XF
Lin
Guohui
G
D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D005821:Genetic Techniques; D016678:Genome; D016679:Genome, Viral; D005838:Genotype; D015497:HIV-1 / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D011994:Recombinant Proteins / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
D011994:Recombinant Proteins