Preferential codon usage in genes

Simon Wain-Hobson*, Ruth Nussinov, Rodney J. Brown, Joel L. Sussman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


We present a method which permits comparison of the preferential use of degenerate codons within any gene. The method makes use of the triplet frequencies in the noncoding frames to assess whether a preference is specific to the reading frame. Preference is given a statistical meaning by use of the analysis of variance coupled to Duncan's multiple range test. Preferential use of degenerate codons is gene-specific and independent of gene size. The data suggest that any correlation between codon frequency distribution and tRNA levels is unreliable. In those animal genes examined, codons ending in C or G are preferred; in animal viruses tested, codons ending in U or A are preferred. Similarly, the bacterial genes and the genes of single-stranded DNA phages that we analyzed differed from each other as well as from eukaryotic genes in the third base of the codon.

Original languageEnglish
Pages (from-to)355-364
Number of pages10
Issue number4
StatePublished - May 1981
Externally publishedYes


  • Duncan's multiple-range test
  • Triplet frequencies
  • analysis of variance
  • noncoding frames


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