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Scaling features of noncoding DNA

Author

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  • Stanley, H.E
  • Buldyrev, S.V
  • Goldberger, A.L
  • Havlin, S
  • Peng, C.-K
  • Simons, M

Abstract

We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range — indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the “redundancy” of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine–guanine (CG) concentration does have a strong “background” effect on redundancy. However, we find that for the purine–pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.

Suggested Citation

  • Stanley, H.E & Buldyrev, S.V & Goldberger, A.L & Havlin, S & Peng, C.-K & Simons, M, 1999. "Scaling features of noncoding DNA," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 273(1), pages 1-18.
    • Handle: RePEc:eee:phsmap:v:273:y:1999:i:1:p:1-18
    DOI: 10.1016/S0378-4371(99)00407-0
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    Citations

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    Cited by:

    1. T. Di Matteo & T. Aste & M. M. Dacorogna, 2003. "Using the Scaling Analysis to Characterize Financial Markets," Papers cond-mat/0302434, arXiv.org.
    2. Lopes, S.R.C. & Nunes, M.A., 2006. "Long memory analysis in DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 361(2), pages 569-588.
    3. Miśkiewicz, Janusz, 2013. "Effects of publications in proceedings on the measure of the core size of coauthors," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(20), pages 5119-5131.
    4. Farzadian, O. & Niry, M.D., 2018. "Role of short-range correlation in facilitation of wave propagation in a long-range ladder chain," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 505(C), pages 49-60.
    5. Möller, Simon & Hameister, Heike & Hütt, Marc-Thorsten, 2014. "A genome signature derived from the interplay of word frequencies and symbol correlations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 414(C), pages 216-226.
    6. Silva, R. & Silva, J.R.P. & Anselmo, D.H.A.L. & Alcaniz, J.S. & da Silva, W.J.C. & Costa, M.O., 2020. "An alternative description of power law correlations in DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 545(C).
    7. Karakatsanis, L.P. & Pavlos, G.P. & Iliopoulos, A.C. & Pavlos, E.G. & Clark, P.M. & Duke, J.L. & Monos, D.S., 2018. "Assessing information content and interactive relationships of subgenomic DNA sequences of the MHC using complexity theory approaches based on the non-extensive statistical mechanics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 505(C), pages 77-93.
    8. Kugiumtzis, D. & Provata, A., 2004. "Statistical analysis of gene and intergenic DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 342(3), pages 623-638.
    9. Saha, Debajyoti & Shaw, Pankaj Kumar & Ghosh, Sabuj & Janaki, M.S. & Sekar Iyengar, A.N., 2018. "Quantification of scaling exponent with Crossover type phenomena for different types of forcing in DC glow discharge plasma," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 490(C), pages 300-310.
    10. Stavros-Richard G. Christopoulos & Nicholas V. Sarlis, 2017. "An Application of the Coherent Noise Model for the Prediction of Aftershock Magnitude Time Series," Complexity, Hindawi, vol. 2017, pages 1-27, February.
    11. Santos, J.V.C. & Moreira, D.M. & Moret, M.A. & Nascimento, E.G.S., 2019. "Analysis of long-range correlations of wind speed in different regions of Bahia and the Abrolhos Archipelago, Brazil," Energy, Elsevier, vol. 167(C), pages 680-687.
    12. Licinio, P & Caligiorne, R.B, 2004. "Inference of phylogenetic distances from DNA-walk divergences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 341(C), pages 471-481.
    13. Pavlos, G.P. & Karakatsanis, L.P. & Iliopoulos, A.C. & Pavlos, E.G. & Xenakis, M.N. & Clark, Peter & Duke, Jamie & Monos, D.S., 2015. "Measuring complexity, nonextensivity and chaos in the DNA sequence of the Major Histocompatibility Complex," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 438(C), pages 188-209.
    14. Farzadian, O. & Niry, M.D., 2016. "Delocalization of mechanical waves in the ladder chain of DNA with correlated disorder," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 450(C), pages 95-103.

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