Comparison of correspondence analysis methods for synonymous codon usage in bacteria

Haruo Suzuki, Celeste J. Brown, Larry J. Forney, Eva M. Top

Research output: Contribution to journalArticlepeer-review

67 Citations (Scopus)


Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.

Original languageEnglish
Pages (from-to)357-365
Number of pages9
JournalDNA Research
Issue number6
Publication statusPublished - 2008 Dec
Externally publishedYes


  • Correspondence analysis
  • Horizontal gene transfer
  • Strand-specific mutational bias
  • Synonymous codon usage
  • Translational selection

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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