Codon volatility does not reflect selective pressure on the HIV-1 genome |
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Authors: | Pillai Satish K Kosakovsky Pond Sergei L Woelk Christopher H Richman Douglas D Smith Davey M |
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Affiliation: | University of California, San Diego, Stein Clinical Research Building, Room 325, 9500 Gilman Drive 0679, La Jolla 92093, USA. |
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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. |
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Keywords: | HIV Codon volatility Selective pressure Evolution |
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