IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v249y1998i1p430-438.html
   My bibliography  Save this article

Analysis of DNA sequences using methods of statistical physics

Author

Listed:
  • Buldyrev, S.V.
  • Dokholyan, N.V.
  • Goldberger, A.L.
  • Havlin, S.
  • Peng, C.-K.
  • Stanley, H.E.
  • Viswanathan, G.M.

Abstract

We review the present status of the studies of DNA sequences using methods of statistical physics. We present evidence, based on systematic studies of the entire GenBank database, supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range, i.e., base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the DNA. We discuss the mechanisms of molecular evolution that may lead to the presence of long-range power-law correlations in noncoding DNA and their absence in coding DNA. One such mechanism is the simple repeat expansion, which recently has attracted the attention of the biological community in conjunction with genetic diseases. We also review new tools – e.g., detrended fluctuation analysis – that are useful for studies of complex hierarchical DNA structure.

Suggested Citation

  • Buldyrev, S.V. & Dokholyan, N.V. & Goldberger, A.L. & Havlin, S. & Peng, C.-K. & Stanley, H.E. & Viswanathan, G.M., 1998. "Analysis of DNA sequences using methods of statistical physics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 249(1), pages 430-438.
    • Handle: RePEc:eee:phsmap:v:249:y:1998:i:1:p:430-438
    DOI: 10.1016/S0378-4371(97)00503-7
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437197005037
    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(97)00503-7?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.

    References listed on IDEAS

    as
    1. Stanley, H.E. & Buldyrev, S.V. & Goldberger, A.L. & Goldberger, Z.D. & Havlin, S. & Mantegna, R.N. & Ossadnik, S.M. & Peng, C.-K. & Simons, M., 1994. "Statistical mechanics in biology: how ubiquitous are long-range correlations?," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 205(1), pages 214-253.
    Full references (including those not matched with items on IDEAS)

    Citations

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


    Cited by:

    1. Dutta, Srimonti & Ghosh, Dipak & Chatterjee, Sucharita, 2016. "Multifractal detrended Cross Correlation Analysis of Foreign Exchange and SENSEX fluctuation in Indian perspective," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 463(C), pages 188-201.
    2. Papapetrou, M. & Kugiumtzis, D., 2013. "Markov chain order estimation with conditional mutual information," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(7), pages 1593-1601.
    3. Jin, Xin & Nie, Rencan & Zhou, Dongming & Yao, Shaowen & Chen, Yanyan & Yu, Jiefu & Wang, Quan, 2016. "A novel DNA sequence similarity calculation based on simplified pulse-coupled neural network and Huffman coding," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 461(C), pages 325-338.
    4. Xie, Rongrong & Deng, Shengfeng & Deng, Weibing & Pato, Mauricio P., 2022. "Generalized Poisson ensemble," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 585(C).
    5. Buldyrev, Sergey V. & Dokholyan, Nikolay V. & Havlin, Shlomo & Stanley, H.Eugene & Stanley, Rachel H.R., 1999. "Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 273(1), pages 19-32.
    6. Kalamaras, N. & Philippopoulos, K. & Deligiorgi, D. & Tzanis, C.G. & Karvounis, G., 2017. "Multifractal scaling properties of daily air temperature time series," Chaos, Solitons & Fractals, Elsevier, vol. 98(C), pages 38-43.
    7. Sidorov, S.P. & Faizliev, A.R. & Balash, V.A. & Korobov, E.A., 2016. "Long-range correlation analysis of economic news flow intensity," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 444(C), pages 205-212.
    8. Chatterjee, Sucharita, 2020. "Analysis of the human gait rhythm in Neurodegenerative disease: A multifractal approach using Multifractal detrended cross correlation analysis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 540(C).
    9. Şahin, Gökhan & Erentürk, Murat & Hacinliyan, Avadis, 2009. "Detrended fluctuation analysis in natural languages using non-corpus parametrization," Chaos, Solitons & Fractals, Elsevier, vol. 41(1), pages 198-205.
    10. Papapetrou, M. & Kugiumtzis, D., 2020. "Tsallis conditional mutual information in investigating long range correlation in symbol sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 540(C).
    11. Chatterjee, Sucharita & Ghosh, Dipak, 2021. "Impact of Global Warming on SENSEX fluctuations — A study based on Multifractal detrended cross correlation analysis between the temperature anomalies and the SENSEX fluctuations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 571(C).
    12. 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.
    13. 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.
    14. 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.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Alvarez-Ramirez, Jose & Espinosa-Paredes, Gilberto & Vazquez, Alejandro, 2005. "Detrended fluctuation analysis of the neutronic power from a nuclear reactor," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 351(2), pages 227-240.
    2. Chiarucci, Riccardo & Ruzzenenti, Franco & Loffredo, Maria I., 2014. "Detecting spatial homogeneity in the World Trade Web with Detrended Fluctuation Analysis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 401(C), pages 1-7.
    3. 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.
    4. Urbanowicz, Krzysztof & Kantz, Holger & Holyst, Janusz A., 2005. "Anti-deterministic behaviour of discrete systems that are less predictable than noise," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 350(2), pages 189-198.
    5. Cizeau, Pierre & Liu, Yanhui & Meyer, Martin & Peng, C.-K. & Eugene Stanley, H., 1997. "Volatility distribution in the S&P500 stock index," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 245(3), pages 441-445.
    6. Podobnik, Boris & Ivanov, Plamen Ch. & Grosse, Ivo & Matia, Kaushik & Eugene Stanley, H., 2004. "ARCH–GARCH approaches to modeling high-frequency financial data," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 344(1), pages 216-220.
    7. 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).
    8. Frank Emmert-Streib, 2013. "Structural Properties and Complexity of a New Network Class: Collatz Step Graphs," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-14, February.
    9. Liu, Yanhui & Cizeau, Pierre & Meyer, Martin & Peng, C.-K. & Eugene Stanley, H., 1997. "Correlations in economic time series," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 245(3), pages 437-440.
    10. Bertrand M. Roehner, 2010. "Fifteen years of econophysics: worries, hopes and prospects," Papers 1004.3229, arXiv.org.
    11. Oikonomou, Thomas & Kaloudis, Konstantinos & Bagci, G. Baris, 2021. "The q-exponentials do not maximize the Rényi entropy," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 578(C).
    12. 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.
    13. Peng, C.-K. & Buldyrev, S.V. & Goldberger, A.L. & Havlin, S. & Mantegna, R.N. & Simons, M. & Stanley, H.E., 1995. "Statistical properties of DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 221(1), pages 180-192.
    14. Riccardo Chiarucci & Franco Ruzzenenti & Maria I. Loffredo, 2013. "Detecting spatial homogeneity in the world trade web with Detrended Fluctuation Analysis," Papers 1308.0526, arXiv.org, revised Nov 2013.
    15. Koscielny-Bunde, Eva & Bunde, Armin & Havlin, Shlomo & Goldreich, Yair, 1996. "Analysis of daily temperature fluctuations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 231(4), pages 393-396.
    16. Zebende, G.F. & Pereira, M.G. & Nogueira Jr., E. & Moret, M.A., 2005. "Universal persistence in astrophysical sources," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 349(3), pages 452-458.
    17. Vitanov, Nikolay K. & Yankulova, Elka D., 2006. "Multifractal analysis of the long-range correlations in the cardiac dynamics of Drosophila melanogaster," Chaos, Solitons & Fractals, Elsevier, vol. 28(3), pages 768-775.
    18. Ortiz-Tánchez, Eduardo & Ebeling, Werner & Lanius, Karl, 2002. "MEI, SOI and mid-range correlations in the onset of El Niño–Southern Oscillation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 310(3), pages 509-520.
    19. Vandewalle, N. & Ausloos, M., 1997. "Coherent and random sequences in financial fluctuations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 246(3), pages 454-459.
    20. Staudacher, M. & Telser, S. & Amann, A. & Hinterhuber, H. & Ritsch-Marte, M., 2005. "A new method for change-point detection developed for on-line analysis of the heart beat variability during sleep," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 349(3), pages 582-596.

    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:249:y:1998:i:1:p:430-438. 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.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with 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.