Analysis of distribution of bases in the coding sequences by a digrammatic technique

Abstract

The frequencies of occurrence of four bases in the first, second and third codon positions and in the total coding sequences have been calculated by the codon usage table published in 1990 by Ikemura et al. The distribution of frequencies are further analysed in detail by a graphic technique presented recently by us. Formulas expressing the frequencies of four bases in the first and second codon positions in terms of frequencies of amino acids have been given. It is shown by the graphic analysis that for 90 species, in the first codon position the purine bases are dominant and in most cases G is the most dominant base. In the second codon position A is the most dominant base, while G is the least dominant base. In the third codon position the G + C content varies from 0.1 to 0.9, keeping the A + C content equal to 1/2 and G content equal to that of C, approximately. If the frequencies for bases A, C, G and U in the total coding sequenses are denoted by a, c, g and u, respectively, it is found that the unequal formula: a² + c² + g² + u² < 1/3, is valid for each of the 90 species including the human and E.coli etc.