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Use and misuse of correspondence analysis in codon usage studies
Guy Perrière1, Jean Thioulouse
1Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. perriere@biomserv.univ-lyon1.fr
Nucleic Acids Research
|October 18, 2002
Summary
Correspondence analysis for codon usage bias can be misused when using relative frequencies. This study highlights issues and proposes alternative methods for accurate translational selection analysis.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Correspondence analysis is commonly applied to codon usage studies.
- Relative codon frequencies are often used to mitigate amino acid composition biases.
- This approach can lead to loss of analytical properties and introduce interpretation errors.
Purpose of the Study:
- To expose the misuse of correspondence analysis in codon usage studies.
- To identify the limitations of using relative codon frequencies.
- To propose alternative strategies for analyzing codon usage biases.
Main Methods:
- Critique of correspondence analysis applied to relative codon frequencies.
- Analysis of codon counts versus relative frequencies.
- Development of alternative analytical strategies.
Main Results:
- Using relative codon frequencies in correspondence analysis can obscure translational selection.
- Misinterpretations can arise, as seen in studies of Borrelia burgdorferi.
- Alternative methods are necessary for accurate codon usage bias assessment.
Conclusions:
- Standard correspondence analysis with relative codon frequencies is problematic for codon usage bias studies.
- Codon counts offer a more informative basis for analysis.
- Alternative strategies are crucial for reliable identification of translational selection.