Preferential codon usage in genes |
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Authors: | Simon Wain-Hobson Ruth Nussinov Rodney J. Brown Joel L. Sussman |
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Affiliation: | 1. Department of Chemical Immunology, The Weizmann Institute of Science, Rehovot Israel;2. Department of Structural Chemistry, The Weizmann Institute of Science, Rehovot Israel;3. Department of Biophysics, The Weizmann Institute of Science, Rehovot Israel |
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Abstract: | 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. |
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Keywords: | Triplet frequencies noncoding frames analysis of variance Duncan's multiple-range test SAS statistical analysis system |
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