A problem in multivariate analysis of codon usage data and a possible solution

Haruo Suzuki, Rintaro Saito, Masaru Tomita

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Multivariate analyses are often used to identify major trends of variation in synonymous codon usage among genes. These analyses need to be performed on properly normalized codon usage data to avoid biases masking this synonymous variation, i.e., gene length, amino acid usage, and codon degeneracy; however, previous studies have failed to do so. In this paper, we demonstrate that the use of alternative normalized data (called 'relative adaptiveness' in the literature) can avoid all these biases and furthermore, can identify more trends of variation among genes, including GC-ending codon usage, GT-ending codon usage, and gene expression level.

Original languageEnglish
Pages (from-to)6499-6504
Number of pages6
JournalFEBS Letters
Volume579
Issue number28
DOIs
Publication statusPublished - 2005 Nov 21

Keywords

  • Amino acid usage
  • Codon degeneracy
  • GC-ending codon usage
  • GT-ending codon usage
  • Gene expression level
  • Gene length
  • Multivariate analysis
  • Principal component analysis
  • Synonymous codon usage

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology

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