Variability Analysis of HIV-1 gp120 V3 Region: I. Point Estimators for the Amino Acid Distribution Characteristics |
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| Authors: | Michael Yu Shchelkanov Alex N Yudin Alex V Antonov Nicole S Starikov Alexander A Vedenov Edward V Karamov |
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| Institution: | 1. Moscow Institute of Physics and Technology, Faculty of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny , Moscow region , 141700 , Russia;2. D. I. Ivanovsky Institute of Virology, Immunochemistry Group , Gamaley 16, Moscow , 123098 , Russia;3. Russian Scientific Center Kurchatov Institute , Kurchatov s., Moscow , 123182 , Russia;4. D. I. Ivanovsky Institute of Virology, Immunochemistry Group , Gamaley 16, Moscow , 123098 , Russia;5. Moscow State University, Institute of Applied Research, Laboratory of Virology , Lenin's Hills, Moscow , 119899 , Russia |
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| Abstract: | 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 consensuses, subconsensuses 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. |
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| Keywords: | DNA ligand adsorption isotherm noise |
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