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Bioinformatics. 2005 Feb 15;21(4):545-7. Epub 2004 Sep 16.

Online synonymous codon usage analyses with the ade4 and seqinR packages.

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  • 1Laboratoire de Biométrie et Biologie Evolutive-CNRS UMR 5558, and INRIA Helix project, Université Claude Bernard-Lyon I 43 bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France.

Abstract

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 Pole 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.

PMID:
15374859
[PubMed - indexed for MEDLINE]
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