Codon volatility does not reflect selective pressure on the HIV-1 genome

Virology. 2005 Jun 5;336(2):137-43. doi: 10.1016/j.virol.2005.03.014.

Abstract

Codon volatility is defined as the proportion of a codon's point-mutation neighbors that encode different amino acids. The cumulative volatility of a gene in relation to its associated genome was recently reported to be an indicator of selection pressure. We used this approach to measure selection on all available full-length HIV-1 subtype B genomes in the Los Alamos HIV Sequence Database, and compared these estimates against those obtained via established likelihood- and distance-based comparative methods. Volatility failed to correlate with the results of any of the comparative methods demonstrating that it is not a reliable indicator of selection pressure.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Biological Evolution
  • Codon / genetics*
  • Genome, Viral
  • HIV-1 / genetics*
  • Likelihood Functions
  • Recombination, Genetic
  • Selection, Genetic*

Substances

  • Codon