Online synonymous codon usage analyses with the ade4 and seqinR packages | Zendy

Delphine Charif | Zendy; Jean Thioulouse | Zendy; Jean R. Lobry | Zendy; Guy Perrière | Zendy

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Online synonymous codon usage analyses with the ade4 and seqinR packages

Author(s) -

Delphine Charif,

Jean Thioulouse,

Jean R. Lobry,

Guy Perrière

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti037

Subject(s) - codon usage bias , computer science , software , web server , web site , confounding , computational biology , biology , genetics , world wide web , genome , gene , statistics , the internet , mathematics , programming language

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.

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