Impact of Tandem repeats on the Scaling of nucleotide Sequences

Techniques such as detrended fluctuation analysis (DFA) and its extensions have been widely used to determine the nature of scaling in nucleotide sequences. In this brief communication we show that tandem repeats which are ubiquitous in nucleotide sequences can prevent reliable estimation of possible long-range correlations. Therefore, it is important to investigate the presence of tandem repeats prior to scaling exponent estimation.

[1]  H. Stanley,et al.  Magnitude and sign correlations in heartbeat fluctuations. , 2000, Physical review letters.

[2]  J. Beckmann,et al.  A gene related to Caenorhabditis elegans spermatogenesis factor fer-1 is mutated in limb-girdle muscular dystrophy type 2B , 1998, Nature Genetics.

[3]  Eivind Coward,et al.  Equivalence of two Fourier methods for biological sequences , 1997 .

[4]  F. Grant,et al.  Nucleotide sequence of the gene coding for human factor VII, a vitamin K-dependent protein participating in blood coagulation. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Radhakrishnan Nagarajan,et al.  Minimizing the Effect of sinusoidal Trends in Detrended Fluctuation Analysis , 2005, Int. J. Bifurc. Chaos.

[6]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[7]  M. Waterman.  Mathematical Methods for DNA Sequences , 1989 .

[8]  Bruce J. West,et al.  Fractal physiology , 1994, IEEE Engineering in Medicine and Biology Magazine.

[9]  H. Prydz,et al.  CpG islands as gene markers in the human genome. , 1992, Genomics.

[10]  Wentian Li,et al.  Long-range correlation and partial 1/fα spectrum in a noncoding DNA sequence , 1992 .

[11]  S Nicolay,et al.  Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation? , 2004, Physical review letters.

[12]  G Bernardi,et al.  CpG islands: features and distribution in the genomes of vertebrates. , 1991, Gene.

[13]  R. Linsker,et al.  A measure of DNA periodicity. , 1986, Journal of theoretical biology.

[14]  C. Peng,et al.  Long-range correlations in nucleotide sequences , 1992, Nature.

[15]  H. Stanley,et al.  Multifractal Detrended Fluctuation Analysis of Nonstationary Time Series , 2002, physics/0202070.

[16]  M. Riley,et al.  IN FRACTAL PHYSIOLOGY , 2022 .

[17]  H. Stanley,et al.  Effect of trends on detrended fluctuation analysis. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[18]  J. Jurka,et al.  Microsatellites in different eukaryotic genomes: survey and analysis. , 2000, Genome research.

[19]  Radhakrishnan Nagarajan,et al.  Minimizing the effect of trends on detrended fluctuation analysis of long-range correlated noise , 2004, cond-mat/0412732.

[20]  S. Havlin,et al.  Detecting long-range correlations with detrended fluctuation analysis , 2001, cond-mat/0102214.