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Variability analysis of HIV-1 gp120 V3 region: II. Hierarchy of taxons
Shchelkanov MYu1, A N Yudin, A V Antonov
1Moscow Institute of Physics and Technology, Faculty of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny, Moscow region, Russia.
Abstract:
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.