Fig. 8.

Appearance and simulation of the codon fine-structure of genomes: in all but the human sequences a fine-structure with a periodicity of 3 bp is present up to window length of several hundred base pairs, which is related to the codon usage (a, b). Already a uniform distribution of the 20 amino acids in artificial random sequences causes this feature. Species-specific codon usage is responsible for the starting behaviour δ(3) < −0.5 or δ(3) > −0.5. Pseudomonas aeruginosa PA01 has an additional dominating periodicity of 12 bp which cannot be explained simply by codon usage (b). The appearance and visibility of the codon usage as well as the degree of correlation at δ(3) is proportional to the concentration c_codon,gene of codons distributed as in the human genome codons within a random sequence and is more apparent for codons organized in genes/blocks (c, for 100% see a). The degree of correlation follows a linear dependence with δ(l = 3, c_codon,gene) = −0.5 + 0.046c_codon,gene and R = 0.99 (d). Organization of codons in genes/blocks leads to a δ(l) maximum and oscillations due to the gene/block length and separation (c, e–g; Fig. 7)