title: Variability analysis of HIV-1 gp120 V3 region: I. Point estimators for the amino acid distribution characteristics.
abstract: Enumerating procedure for symbol sequences is proposed. Relationship between Hamming distance for symbol sequences and Euclidean distance for corresponding enumerations is established, and more universal Hamming-transformed Euclidean measure is constructed. A distribution function of amino acid substitutions and some of its point estimators (consensus, subconsensus, sample mean, sample central moments and asymmetry coefficient) are introduced. Hamming-transformed Euclidean measures between consensus, subconsensus and sample means for ten HIV-1 taxons of gp120 V3 regions are calculated. It is demonstrated that these taxons have a complicated pattern which is significant for their classification.
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: N S
authors.initials: NS
authors.lastname: Starikov
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; D000596:Amino Acids / Q000032:analysis; D016384:Consensus Sequence; D014644:Genetic Variation / Q000235:genetics*; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics*; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics*; D008433:Mathematics; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics*
chemical_list: D000596:Amino Acids; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments