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Bioinformatics Advance Access originally published online on September 16, 2004
Bioinformatics 2005 21(4):545-547; doi:10.1093/bioinformatics/bti037
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Bioinformatics vol. 21 issue 4 © Oxford University Press 2005; all rights reserved.

Online synonymous codon usage analyses with the ade4 and seqinR packages

D. Charif , J. Thioulouse , J. R. Lobry * and G. Perrière

Laboratoire de Biométrie et Biologie Évolutive—CNRS UMR 5558, and INRIA Helix project, Université Claude Bernard—Lyon I 43 bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France

*To whom correspondence should be addressed.

Summary: 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 http://pbil.univ-lyon1.fr/datasets/charif04/ with a demo allowing us to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence.

Contact: http://pbil.univ-lyon1.fr/members/lobry


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 DNA ResHome page
H. Suzuki, C. J. Brown, L. J. Forney, and E. M. Top
Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria
DNA Res, December 1, 2008; 15(6): 357 - 365.
[Abstract] [Full Text] [PDF]


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