Variability analysis of HIV-1 gp120 V3 region: I. Point estimators for the amino acid distribution characteristics

J Biomol Struct Dyn. 1997 Oct;15(2):217-29. doi: 10.1080/07391102.1997.10508187.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / analysis
  • Consensus Sequence
  • Genetic Variation / genetics*
  • HIV Envelope Protein gp120 / chemistry
  • HIV Envelope Protein gp120 / genetics*
  • HIV-1 / chemistry
  • HIV-1 / genetics*
  • Mathematics
  • Molecular Sequence Data
  • Peptide Fragments / chemistry
  • Peptide Fragments / genetics*

Substances

  • Amino Acids
  • HIV Envelope Protein gp120
  • HIV envelope protein gp120 (305-321)
  • Peptide Fragments