Characterizing large scale base composition structures of genomes

Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed turbulence [She and Lévêque, Phys. Rev. Lett. 72, 336 (1994)]. Large scale (10 ≤ l ≤ 10 bp) base density fluctuation is shown to satisfy the HS similarity. The derived values of a HS parameter β from a large number of genome data (including Bacteria, Archaea, human chromosomes and viruses) characterize different biological properties such as strand symmetry, phylogenetic relations and horizontal gene transfer. It is suggested that the HS analysis offers a useful quantitative description for heterogeneity, sequence complexity and large scale structures of genomes.