Long-range correlations in DNA sequences using 2D DNA walk based on pairs of sequential nucleotides

Abstract

Abstract We study the long-range correlations of DNA sequences using two-dimensional (2D) DNA walk model by considering pairs of sequential nucleotides. In this model, the effects of second-order correlation of DNA sequences on long-range correlations are considered. Some linear correlations are obtained in the double logarithmic plots of the mean square distance 〈R2(l)〉 and fluctuation F(l) versus nucleotide distance l along the DNA chain. It is found that 〈R2(l)〉 and F(l) may be expressed as 〈R 2 (l)〉∼l γ F(l)∼l H The power spectrums of several sequential nucleotide pairs are also studied, and these curves are flat and hardly changed when the frequency f 0.15 bp−1). There is a notable peak value, which occurs at a frequency of 0.333 for coding DNA sequences, while the same peak value is not obtained for non-coding DNA sequences. The autocorrelation function C(l) is also calculated. Each curve of the double logarithmic plot has an almost linear correlation in the low value l region, especially in Escherichia coli genomic DNA. For non-coding DNA sequence, the curves have no-linear tails when l>2.0×104.