Confidence interval for the number of selectively neutral amino acid polymorphisms - PubMed (original) (raw)
Confidence interval for the number of selectively neutral amino acid polymorphisms
S A Sawyer et al. Proc Natl Acad Sci U S A. 1987 Sep.
Abstract
A statistical approach to the analysis of DNA sequences has been developed, which provides a confidence interval estimate for the proportion of naturally occurring amino acid polymorphisms that are selectively neutral. When applied to the gnd gene coding for 6-phosphogluconate dehydrogenase in a sample of seven natural isolates of Escherichia coli, the method indicates that the proportion of observed amino acid polymorphisms that are selectively neutral is unlikely to be greater than 49% (upper 95% confidence limit). On the other hand, the observations are also consistent with a model in which all of the observed amino acid substitutions are mildly deleterious with an average selection coefficient approximating 1.6 X 10(-7). Various models for the distribution of configurations at silent sites are also investigated.
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References
- Genetics. 1978 Jan;88(1):171-9 - PubMed
- Nature. 1974 Nov 29;252(5482):351-4 - PubMed
- Mol Biol Evol. 1985 Mar;2(2):150-74 - PubMed
- Proc Natl Acad Sci U S A. 1980 Nov;77(11):6710-4 - PubMed
- Genetics. 1980 Dec;96(4):801-17 - PubMed
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