Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA |
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Authors: | Lars S Jermiin Peter G Foster Dan Graur Roger M Lowe Ross H Crozier |
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Institution: | (1) Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada, CA;(2) Department of Zoology, George S Wise Faculty of Life Science, Tel Aviv University, Ramat Aviv 69978, Israel, IL;(3) School of Genetics and Human Variation, La Trobe University, Bundoora, Victoria 3083, Australia, AU |
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Abstract: | The most generally applicable procedure for obtaining estimates of the symmetrical, or strand-nonspecific, directional mutation
pressure (μD) on protein-coding DNA sequences is to determine the G+C content at synonymous codon sites (P
syn), and to divide P
syn by twice the arithmetic mean of the G+C content at synonymous codon sites of a large number of randomly generated, synonymously
coding DNA sequences (P
syn). Unfortunately, the original procedure yields biased estimates of P
syn and μD and is computationally expensive. We here present a fast procedure for estimating unbiased μD values. The procedure employs direct calculation of P
syn (≈P
syn) and two normalization procedures, one for P
syn≤P
syn and another for P
syn≥P
syn. The normalization removes a bias sometimes caused by codons specifying arginine, asparagine, isoleucine, and leucine. Consequently,
comparison of protein-coding genes that are translated using different genetic codes is facilitated.
Received: 5 May 1995 / Accepted: 30 November 1995 |
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Keywords: | : Symmetrical directional mutation pressure — A+T pressure — G+C pressure — Synonymous codon sites — Nonsynonymous codon sites — Bias correction |
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