title: Nonlinear analysis of correlations in Alu repeat sequences in DNA.
abstract: We report on a nonlinear analysis of deterministic structures in Alu repeats, one of the richest repetitive DNA sequences in the human genome. Alu repeats contain the recognition sites for the restriction endonuclease AluI, which is what gives them their name. Using the nonlinear prediction method developed in chaos theory, we find that all Alu repeats have novel deterministic structures and show strong nonlinear correlations that are absent from exon and intron sequences. Furthermore, the deterministic structures of Alus of younger subfamilies show panlike shapes. As young Alus can be seen as mutation free copies from the "master genes," it may be suggested that the deterministic structures of the older subfamilies are results of an evolution from a "panlike" structure to a more diffuse correlation pattern due to mutation.
authors.affiliation: Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xiao
authors.forename: Yanzhao
authors.initials: Y
authors.lastname: Huang
authors.forename: Mingfeng
authors.initials: M
authors.lastname: Li
authors.forename: Ruizhen
authors.initials: R
authors.lastname: Xu
authors.forename: Saifeng
authors.initials: S
authors.lastname: Xiao
mesh_terms: D020087:Alu Elements; D004247:DNA / Q000737:chemistry*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000494:pharmacology; D005091:Exons; D015894:Genome, Human; D006801:Humans; D007438:Introns; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D009154:Mutation; D017711:Nonlinear Dynamics; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA; C024669:endodeoxyribonuclease AluI; D015252:Deoxyribonucleases, Type II Site-Specific