Codon volatility does not reflect selective pressure on the HIV-1 genome
Codon volatility does not reflect selective pressure on the HIV-1 genome
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.
hiv, codon volatility, selective pressure, evolution
137-143
Pillai, Satish K.
aabef249-ae99-43bc-bbc6-e2c957d4015a
Kosakovsky Pond, Sergei L.
3b6d08b2-b554-47c0-9070-914b941fb75f
Woelk, Christopher H.
4d3af0fd-658f-4626-b3b5-49a6192bcf7d
Richman, Douglas D.
978207ff-1609-4247-96c6-b269b743ea14
Smith, Davey M.
3a82ac7f-ef1a-4999-90d3-7520981e81fd
5 June 2005
Pillai, Satish K.
aabef249-ae99-43bc-bbc6-e2c957d4015a
Kosakovsky Pond, Sergei L.
3b6d08b2-b554-47c0-9070-914b941fb75f
Woelk, Christopher H.
4d3af0fd-658f-4626-b3b5-49a6192bcf7d
Richman, Douglas D.
978207ff-1609-4247-96c6-b269b743ea14
Smith, Davey M.
3a82ac7f-ef1a-4999-90d3-7520981e81fd
Pillai, Satish K., Kosakovsky Pond, Sergei L., Woelk, Christopher H., Richman, Douglas D. and Smith, Davey M.
(2005)
Codon volatility does not reflect selective pressure on the HIV-1 genome.
Virology, 336 (2), .
(doi:10.1016/j.virol.2005.03.014).
(PMID:15892955)
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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e-pub ahead of print date: 14 April 2005
Published date: 5 June 2005
Keywords:
hiv, codon volatility, selective pressure, evolution
Organisations:
Clinical & Experimental Sciences
Identifiers
Local EPrints ID: 352761
URI: http://eprints.soton.ac.uk/id/eprint/352761
ISSN: 0042-6822
PURE UUID: 479960e1-cca3-4c8e-b675-1c4312805dac
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Date deposited: 10 Jun 2013 14:16
Last modified: 14 Mar 2024 13:56
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Contributors
Author:
Satish K. Pillai
Author:
Sergei L. Kosakovsky Pond
Author:
Christopher H. Woelk
Author:
Douglas D. Richman
Author:
Davey M. Smith
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