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Improved Prediction of Coreceptor Usage and Phenotype of HIV-1 Based on Combined Features of V3 Loop Sequence Using Random Forest  

Xu, Shungao (Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology)
Huang, Xinxiang (Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology)
Xu, Huaxi (Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology)
Zhang, Chiyu (Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology)
Publication Information
Journal of Microbiology / v.45, no.5, 2007 , pp. 441-446 More about this Journal
Abstract
HIV-1 coreceptor usage and phenotype mainly determined by V3 loop are associated with the disease progression of AIDS. Predicting HIV-1 coreceptor usage and phenotype facilitates the monitoring of R5-to-X4 switch and treatment decision-making. In this study, we employed random forest to predict HIV-1 biological phenotype, based on 37 random features of V3 loop. In comparison with PSSM method, our RF predictor obtained higher prediction accuracy (95.1% for coreceptor usage and 92.1% for phenotype), especially for non-B non-C HIV-l subtypes (96.6% for coreceptor usage and 95.3% for phenotype). The net charge, polarity of V3 loop and five V3 sites are seven most important features for predicting HIV-1 coreceptor usage or phenotype. Among these features, V3 polarity and four V3 sites (22, 12, 18 and 13) are first reported to have high contribution to HIV-1 biological phenotype prediction.
Keywords
HIV-1; V3 loop; random forest; cereceptor; phenotype; net charge;
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