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


BACKGROUND
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.


BACKGROUND
http://pbil.univ-lyon1.fr/members/lobry.
Charif
D
D
Laboratoire 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.
Thioulouse
J
J
Lobry
J R
JR
Perrière
G
G
D000465:Algorithms; D003062:Codon / Q000235:genetics*; D003196:Computer Graphics; D009862:Online Systems; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D003062:Codon