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 sequences are denoted by a, c, g and u, respectively, it is found that the unequal formula: a2 + c2 + g2 + u2 less than 1/3, is valid for each of the 90 species including the human and E.coli etc.

Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences

“…This observation confirms already known ''invariants'' of codon usage described in Refs. [30][31][32].…”

Identification of replication origins in archaeal genomes based on the Z‐curve method

“…The Z-curve is composed of a series of nodes, P 0 , P 1 , P 2 , ..., P N , with coordinates x n , y n and z n (n = 0, 1, 2, …, N, where N is the length of the DNA sequence), which are uniquely determined by the Z-transform of a DNA sequence (Zhang and Zhang 1991, 1994):…”

Genomic Islands in theCorynebacterium efficiensGenome

“…where A n , C n , G n , and T n are the cumulative numbers of the bases A, C, G, and T, respectively, occurring in the subsequence from the first base to the nth base in the inspected DNA sequence with length N. z n is one of the components of the Z curve, which is a three-dimensional curve that uniquely represents a DNA sequence (13,16). To amplify the deviations of z n , the curve of z n ϳ n is fitted by a straight line by the least-squares technique,…”