Online synonymous codon usage analyses with the ade4 and seqinR packages.
other · Level V
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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 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. http://pbil.univ-lyon1.fr/members/lobry.
Medical subject headings
- Algorithms
- Codon
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Software
- User-Computer Interface