Variability Analysis of HIV-1 gp120 V3 Region: II. Hierarchy of Taxons

• Published in: Journal of biomolecular structure & dynamics Vol. 15; no. 2; pp. 231 - 241
• Main Authors: Shchelkanov, Michael Yu, Yudin, Alex N., Antonov, Alex V., Soinov, Lev A., Zalunin, Vadim V., Vedenov, Alexander A., Karamov, Edward V.
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis Group 01.10.1997
• Subjects: AIDS/HIV; Amino Acid Sequence; Cluster Analysis; Genetic Variation - genetics; HIV Envelope Protein gp120 - chemistry; HIV Envelope Protein gp120 - genetics; HIV-1 - chemistry; HIV-1 - classification; HIV-1 - genetics; Mathematics; Peptide Fragments - chemistry; Peptide Fragments - genetics
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.1997.10508188

In the previous work (M. Yu. Shchelkanov, A. N. Yudin, A. V. Antonov, N. S. Starikov, A. A. Vedenov, E. V. Karamov, J. Biomol. Struct. Dyn. 15, 217-229 (1997)) we have introduced the amino acid distribution function within HIV-1 taxons and Hamming-transformed Euclidean measures between their characteristics: consensus, subconsensus and sample mean. In this work the referred characteristics are used for hierarchical classification of amino acid sequences of gp120 V3 region belonging to different HIV-1 taxons. A comparative analysis of the results produced by various classification methods is carried out. Multidimensional scaling of distance matrix for the specified characteristics is used to visualize the pattern of HIV-1 variability.