Variability analysis of HIV-1 gp120 V3 region: II. Hierarchy of taxons.
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.
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
Soinov
L A
LA
Zalunin
V V
VV
Vedenov
A A
AA
Karamov
E V
EV
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*
D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments