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Online synonymous codon usage analyses with the ade4 and seqinR packages
Bioinformatics, to be published
D. Charif, J. Thioulouse, J.R. Lobry, G. Perrière


Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability in amino acid composition between proteins is a confounding factor when one wants to analyse synonymous codon usage variability. A simple and natural way to cope with this problem is to use within-group correspondence analysis. There is, however, no user-friendly implementation of this method available for genomic studies. Our motivation was to provide to the community a Web facility to easily study synonymous codon usage on a subset of data available in public genomic databases. Availability: Availability through the Pôle Bioinformatique Lyonnais (PBIL) Web server at with a demo allowing to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence.

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