title: Codon volatility does not reflect selective pressure on the HIV-1 genome.
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.
authors.affiliation: University of California, San Diego, Stein Clinical Research Building, Room 325, 9500 Gilman Drive 0679, La Jolla 92093, USA.
authors.forename: Satish K
authors.initials: SK
authors.lastname: Pillai
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Kosakovsky Pond
authors.forename: Christopher H
authors.initials: CH
authors.lastname: Woelk
authors.forename: Douglas D
authors.initials: DD
authors.lastname: Richman
authors.forename: Davey M
authors.initials: DM
authors.lastname: Smith
mesh_terms: D005075:Biological Evolution; D003062:Codon / Q000235:genetics*; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D016013:Likelihood Functions; D011995:Recombination, Genetic; D012641:Selection, Genetic
chemical_list: D003062:Codon