title: Variability analysis of HIV-1 gp120 V3 region: II. Hierarchy of taxons.
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.
authors.affiliation: Moscow Institute of Physics and Technology, Faculty of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny, Moscow region, Russia.
authors.lastname: Shchelkanov MYu
authors.forename: A N
authors.initials: AN
authors.lastname: Yudin
authors.forename: A V
authors.initials: AV
authors.lastname: Antonov
authors.forename: L A
authors.initials: LA
authors.lastname: Soinov
authors.forename: V V
authors.initials: VV
authors.lastname: Zalunin
authors.forename: A A
authors.initials: AA
authors.lastname: Vedenov
authors.forename: E V
authors.initials: EV
authors.lastname: Karamov
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D014644:Genetic Variation / Q000235:genetics*; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics*; D015497:HIV-1 / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D008433:Mathematics; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics*
chemical_list: D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments