Nucleic Acids Research, 2002, Vol. 30, No. 20 4548-4555
© 2002 Oxford University Press
Use and misuse of correspondence analysis in codon usage studies
Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard – Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
*To whom correspondence should be addressed. Tel: +33 472 44 62 96; Fax: +33 478 89 27 19; Email: perriere{at}biomserv.univ-lyon1.fr
Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on codon usage, it is common to use tables containing relative codon frequencies (or ratios of frequencies) instead of simple codon counts to get rid of these amino acid biases. The problem is that some important properties of correspondence analysis, such as rows weighting, are lost in the process. Moreover, the use of relative measures sometimes introduces other biases and often diminishes the quantity of information to analyse, occasionally resulting in interpretation errors. For instance, in the case of an organism such as Borrelia burgdorferi, the use of relative measures led to the conclusion that there was no translational selection, while analyses based on codon counts show that there is a possibility of a selective effect at that level. In this paper, we expose these problems and we propose alternative strategies to correspondence analysis for studying codon usage biases when amino acid composition effects must be removed.
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