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Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid
Shchelkanov MYu1, N S Starikov, I V Yaroslavtsev
1Moscow Institute of Physics and Technology, Faculty of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny, Moscow region, Russia.
Abstract:
Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures for HIV-1 V3 classification. Two-mode distribution for the subtype E could sertificate that this subtype includes two thinner taxons.