An evaluation of measures of synonymous codon usage bias

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 d...

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Bibliographic Details
Published in:Journal of molecular evolution 1998-09, Vol.47 (3), p.268-274
Main Authors: Comeron, J M, Aguadé, M
Format: Article
Language:English
Subjects:
Amino acids
Animals
Base Composition
Base Sequence
Codon - genetics
Computer Simulation
Deoxyribonucleic acid
DNA
Drosophila melanogaster - genetics
Escherichia coli - genetics
Evolutionary biology
Genes, Bacterial
Genes, Fungal
Genes, Insect - genetics
Genetics
Molecular biology
Saccharomyces cerevisiae - genetics
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Summary: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.
ISSN:0022-2844
1432-1432
DOI:10.1007/pl00006384