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.
State Key Lab for Turbulence and Complex Systems and Center for Theoretical Biology, Peking University, Beijing 100871, China.
Zhengqing
Z
Ouyang
Chao
C
Wang
Zhen-Su
ZS
She
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