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Bioinformatics Advance Access published online on September 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti037
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 6, 2004
Revised June 22, 2004
Accepted July 23, 2004

Article

Online synonymous codon usage analyses with the ade4 and seqinR packages

D. Charif 1, J. Thioulouse 1, J. R. Lobry 1*, and G. Perrière 1

1 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. E-mail: http://pbil.univ-lyon1.fr/members/lobry/.


  Abstract

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 to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence.


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