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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.

Citation

X. Wu, R. Goebel, X. Wan, G. Lin. "Whole Genome Composition Distance for Hiv-1 Genotyping". Life Science Society Computational Systems Bioinformatics Conference, pp 179-190, April 2006.

Keywords: machine learning
Category: In Conference

BibTeX

@incollection{Wu+al:LSSCSB06,
  author = {Xiaomeng Wu and Randy Goebel and Xiu-Feng Wan and Guohui Lin},
  title = {Whole Genome Composition Distance for Hiv-1 Genotyping},
  Pages = {179-190},
  booktitle = {Life Science Society Computational Systems Bioinformatics
    Conference},
  year = 2006,
}

Last Updated: March 14, 2007
Submitted by Nelson Loyola

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