Scaling and hierarchical structures in DNA sequences.
A method of analyzing DNA correlation structure is introduced. Density fluctuations of nucleotides are shown to display an extended self-similarity scaling when the scale varies between 100 and 8000 base pairs. The scaling is accurately described by a hierarchical structure model of She and Leveque [Phys. Rev. Lett. 72, 336 (1994)]]. The derived model parameter beta is able to quantify moderately large-scale correlations which exist in a true DNA sequence but are absent in its randomly shuffled sequence and in a simulated model sequence by an evolution model of Hsieh et al. [Phys. Rev. Lett. 90, (2003)]]. Finally, it is shown that beta varies with the evolution category and measures the organizational complexity of the genome.
Ouyang
Zhengqing
Z
State Key Lab for Turbulence and Complex Systems and Center for Theoretical Biology, Peking University, Beijing 100871, China.
Wang
Chao
C
She
Zhen-Su
ZS
D000818:Animals; D055592:Biophysical Phenomena; D001703:Biophysics; D002875:Chromosomes / Q000648:ultrastructure; D004247:DNA / Q000737:chemistry*; D019992:Databases as Topic; D005800:Genes, Fungal; D006801:Humans; D009690:Nucleic Acid Conformation
D004247:DNA