Journal of Molecular Evolution

, Volume 47, Issue 3, pp 268–274

An Evaluation of Measures of Synonymous Codon Usage Bias

  • Josep M.  Comeron
  • Montserrat  Aguadé

DOI: 10.1007/PL00006384

Cite this article as:
Comeron, J. & Aguadé, M. J Mol Evol (1998) 47: 268. doi:10.1007/PL00006384


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.

Key words: Synonymous codon usage bias — Estimation methods — Effective number of codons — Codon bias index — Codon adaptation index — ``Scaled'' χ2— Intrinsic codon bias index 

Copyright information

© Springer-Verlag New York Inc. 1998

Authors and Affiliations

  • Josep M.  Comeron
    • 1
  • Montserrat  Aguadé
    • 1
  1. 1.Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, 08071 Barcelona, SpainES

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