WHOLE GENOME COMPOSITION DISTANCE FOR HIV-1 GENOTYPING

Xiaomeng Wu, Randy Goebel, Xiu-Feng Wan, Guohui Lin*

Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada. ghlin@cs.ualberta.ca

Comput Syst Bioinformatics Conf. August, 2006. Vol. 5, p. 179-190. Full-Text PDF

*To whom correspondence should be addressed.

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.