Niveau: Supérieur, Doctorat, Bac+8
Use and misuse of correspondence analysis in codon usage studies Guy Perrie Á re* and Jean Thioulouse Laboratoire de Biome  trie et Biologie E  volutive, UMR CNRS 5558, Universite  Claude Bernard ± Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France Received May 17, 2002; Revised July 10, 2002; Accepted August 22, 2002 ABSTRACT 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 corres- pondence 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 ana- lyse, 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.
- membrane protein
- codon usage
- table containing
- genes
- contingency table
- when using
- shock-like protein
- amino acid
- codon composition