One-parameter discrete model of the genetic diversity.

One-parameter discrete model estimating genetic distance between precursor and descendant nucleotide sequences after several steps of substitution acts is developed. This model based on the previously introduced symbol sequences enumeration procedure (M.Y.

Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid hamming distances.

Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures for HIV-1 V3 classification.

Variability analysis of HIV-1 gp120 V3 region: III. Distinctions between various sets of peptide fragments derived from the sequences belonging to different HIV-1 taxons.

Distinction criterion for various sets of fixed length peptide fragments and integral distinction measure for various sets of peptide fragments with different length and start position ranges have been introduced on the base of an enumeration procedure and a point estimators for the amino acid distribution characteristics introduced previously (M. Yu. Shchelkanov, A.

Variability analysis of HIV-1 gp120 V3 region: II. Hierarchy of taxons.

In the previous work (M. Yu. Shchelkanov, A.

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.