| Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loop sequence using random forest. | |
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MedLine Citation:
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PMID: 17978804 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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-1 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. |
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Authors:
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Shungao Xu; Xinxiang Huang; Huaxi Xu; Chiyu Zhang |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Journal of microbiology (Seoul, Korea) Volume: 45 ISSN: 1225-8873 ISO Abbreviation: J. Microbiol. Publication Date: 2007 Oct |
Date Detail:
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Created Date: 2007-11-05 Completed Date: 2007-12-06 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9703165 Medline TA: J Microbiol Country: Korea (South) |
Other Details:
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Languages: eng Pagination: 441-6 Citation Subset: IM |
Affiliation:
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Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology, Zhenjiang, Jiangsu, PR China. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Amino Acid Sequence HIV Envelope Protein gp120 / chemistry*, classification, genetics HIV-1 / classification, genetics* Molecular Sequence Data Peptide Fragments / chemistry*, classification, genetics Phenotype Receptors, HIV / genetics, physiology* Software |
| Chemical | |
Reg. No./Substance:
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0/HIV Envelope Protein gp120; 0/HIV envelope protein gp120 (305-321); 0/Peptide Fragments; 0/Receptors, HIV |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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