An Evaluation of Measures of Synonymous Codon Usage Bias |
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Authors: | Josep M Comeron Montserrat Aguadé |
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Institution: | (1) Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, 08071 Barcelona, Spain, ES |
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Abstract: | Synonymous codons are not generally used at equal frequencies, and this trend is observed for most genes and organisms. Several
methods have been proposed and used to estimate the degree of the nonrandom use of the different synonymous codons. The estimates
obtained by these methods, however, show different levels of both precision and dispersion when coding regions of a finite
number of codons are under analysis. Here, we present a study, based on computer simulation, of how the different methods
proposed to evaluate the nonrandom use of synonymous codons are affected by the length of the coding region analyzed. The
results show that some of these methods are heavily influenced by the number of codons and that the comparison of codon usage
bias between coding regions of different lengths shows a methodological bias under different conditions of nonrandom use of
synonymous codons. The study of the dispersion of the estimates obtained by the different methods gives, on the other hand,
an indication of the methods to be applied to compare values of codon usage bias among coding regions of equivalent length.
Received: 10 September 1997 / Accepted: 23 March 1998 |
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Keywords: | : Synonymous codon usage bias — Estimation methods — Effective number of codons — Codon bias index — Codon adaptation index — ``Scaled' χ 2— Intrinsic codon bias index |
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