IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v273y1999i1p1-18.html
   My bibliography  Save this article

Scaling features of noncoding DNA

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437199004070
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/S0378-4371(99)00407-0?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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. 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).
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:273:y:1999:i:1:p:1-18. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.