IDEAS home Printed from https://ideas.repec.org/a/wsi/ijmpcx/v21y2010i01ns0129183110014975.html
   My bibliography  Save this article

Differentiating The Protein Coding And Noncoding Rna Segments Of Dna Using Shannon Entropy

Author

Listed:
  • P. MAZAHERI

    (Interdisciplinary Neuroscience Research Program (INRP) — Tehran University of Medical Sciences, Tehran, Iran;
    Tehran University of Medical Sciences, 13145 Tehran, Iran)

  • A. H. SHIRAZI

    (Interdisciplinary Neuroscience Research Program (INRP) — Tehran University of Medical Sciences, Tehran, Iran;
    Tehran University of Medical Sciences, 13145 Tehran, Iran)

  • N. SAEEDI

    (Interdisciplinary Neuroscience Research Program (INRP) — Tehran University of Medical Sciences, Tehran, Iran;
    Tehran University of Medical Sciences, 13145 Tehran, Iran)

  • G. REZA JAFARI

    (Department of Physics, Shahid Beheshti University, G. C., Evin, Tehran 19839, Iran;
    Department of Nano-science, IPM, P. O. Box 19395-5531, Tehran, Iran)

  • MUHAMMAD SAHIMI

    (Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA)

Abstract

The complexity of DNA sequences is evaluated in order to differentiate between protein-coding and noncoding RNA segments. The method is based on computing the Shannon entropy of the sequences. By comparing the entropy of the original sequence with that of its shuffled one, we identify the source of the difference between the two segments and their relative contributions to the sequence. To demonstrate the method, the DNA sequences of the bacteriumClostridium difficile 630(G + C = 29.1%)andBdellovibrio bacteriovorus(G + C = 50.6%)are analyzed, which are representatives of bacteria with unbalanced and balanced nucleotide content, respectively. It is shown that in both bacteria, regardless of nucleotide content,ΔrS— the relative difference of the two entropies — is significantly greater in protein-coding regions, when compared with noncoding RNA segments.

Suggested Citation

  • P. Mazaheri & A. H. Shirazi & N. Saeedi & G. Reza Jafari & Muhammad Sahimi, 2010. "Differentiating The Protein Coding And Noncoding Rna Segments Of Dna Using Shannon Entropy," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 21(01), pages 1-9.
    • Handle: RePEc:wsi:ijmpcx:v:21:y:2010:i:01:n:s0129183110014975
    DOI: 10.1142/S0129183110014975
    as

    Download full text from publisher

    File URL: http://www.worldscientific.com/doi/abs/10.1142/S0129183110014975
    Download Restriction: Access to full text is restricted to subscribers
    File URL: https://libkey.io/10.1142/S0129183110014975?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.

    More about this item

    Keywords

    DNA Sequence; Shannon Entropy;

    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:wsi:ijmpcx:v:21:y:2010:i:01:n:s0129183110014975. 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: Tai Tone Lim (email available below). General contact details of provider: http://www.worldscinet.com/ijmpc/ijmpc.shtml .

    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.