Title: Detecting molecular selection on single amino acid replacements

Authors: David A. McClellan

Addresses: Bigelow Laboratory for Ocean Sciences, PO Box 475, 180 McKown Point Road, West Boothbay Harbor, Maine, 04575 – 0475, USA

Abstract: Amino acid property methods have repeatedly proven more sensitive than nucleotide-based methods, especially to the subtle influences of selection on Single Nucleotide Polymorphisms (SNPs). The purpose of this study is to evaluate the effects of population sampling and sliding window size on the sensitivity of one amino acid based method by assessing drug resistant SNPs from the HIV-1 gag-pol gene. The analysis of most of the SNPs produced positive results. There was not a trend in terms of properties affected most often, but sliding window size affected results more than population sampling.

Keywords: amino acid properties; drug resistant SNPs; single nucleotide polymorphisms; positive selection; adaptation; HIV-1; drug resistance; molecular selection; population sampling; sliding window size; bioinformatics; HIV.

DOI: 10.1504/IJBRA.2012.045977

International Journal of Bioinformatics Research and Applications, 2012 Vol.8 No.1/2, pp.67 - 80

Published online: 05 Dec 2014 *

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