Variability analysis of HIV-1 gp120 V3 region: I. Point estimators for the amino acid distribution characteristics.
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.
Shchelkanov MYu
Moscow Institute of Physics and Technology, Faculty of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny, Moscow region, Russia.
Yudin
A N
AN
Antonov
A V
AV
Starikov
N S
NS
Vedenov
A A
AA
Karamov
E V
EV
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*
D000596:Amino Acids; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments