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Journal of Molecular Evolution

, Volume 42, Issue 4, pp 476–480 | Cite as

Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA

  • Lars S. Jermiin
  • Peter G. Foster
  • Dan Graur
  • Roger M. Lowe
  • Ross H. Crozier
Letter To The Editor

Abstract

The most generally applicable procedure for obtaining estimates of the symmetrical, or strand-nonspecific, directional mutation pressure (μ D) on protein-coding DNA sequences is to determine the G+C content at synonymous codon sites (P syn), and to divideP 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 (\(\bar P_{syn} \)). Unfortunately, the original procedure yields biased estimates ofP syn andμ D and is computationally expensive. We here present a fast procedure for estimating unbiasedμ D values. The procedure employs direct calculation of\(\hat P_{syn} ( \approx \bar P_{syn} )\) and two normalization procedures, one for\(P_{syn} \leqslant \hat P_{syn} \) and another for\(P_{syn} \geqslant \hat P_{syn} \). 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.

Key words

Symmetrical directional mutation pressure A+T pressure G+C pressure Synonymous codon sites Nonsynonymous codon sites Bias correction 

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Copyright information

© Springer-Verlag New York Inc. 1996

Authors and Affiliations

  • Lars S. Jermiin
    • 1
  • Peter G. Foster
    • 1
  • Dan Graur
    • 2
  • Roger M. Lowe
    • 3
  • Ross H. Crozier
    • 3
  1. 1.Department of BiologyUniversity of OttawaOttawaCanada
  2. 2.Department of Zoology, George S Wise Faculty of Life ScienceTel Aviv UniversityRamat AvivIsrael
  3. 3.School of Genetics and Human VariationLa Trobe UniversityBundooraAustralia

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