IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v454y2016icp117-128.html
   My bibliography  Save this article

Codon information value and codon transition-probability distributions in short-term evolution

Author

Listed:
  • Jiménez-Montaño, M.A.
  • Coronel-Brizio, H.F.
  • Hernández-Montoya, A.R.
  • Ramos-Fernández, A.

Abstract

To understand the way the Genetic Code and the physical–chemical properties of coded amino acids affect accepted amino acid substitutions in short-term protein evolution, taking into account only overall amino acid conservation, we consider an underlying codon-level model. This model employs codon pair-substitution frequencies from an empirical matrix in the literature, modified for single-base mutations only. Ordering the degenerated codons according to their codon information value (Volkenstein, 1979), we found that three-fold and most of four-fold degenerated codons, which have low codon values, were best fitted to rank-frequency distributions with constant failure rate (exponentials). In contrast, almost all two-fold degenerated codons, which have high codon values, were best fitted to rank-frequency distributions with variable failure rate (inverse power-laws). Six-fold degenerated codons are considered to be doubly assigned. The exceptional behavior of some codons, including non-degenerate codons, is discussed.

Suggested Citation

  • Jiménez-Montaño, M.A. & Coronel-Brizio, H.F. & Hernández-Montoya, A.R. & Ramos-Fernández, A., 2016. "Codon information value and codon transition-probability distributions in short-term evolution," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 454(C), pages 117-128.
    • Handle: RePEc:eee:phsmap:v:454:y:2016:i:c:p:117-128
    DOI: 10.1016/j.physa.2016.02.043
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437116002090
    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/j.physa.2016.02.043?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. Anthony D. Keefe & Jack W. Szostak, 2001. "Functional proteins from a random-sequence library," Nature, Nature, vol. 410(6829), pages 715-718, April.
    2. Kim, J.K. & Yang, S.I. & Kwon, Y.H. & Lee, E.I., 2005. "Codon and amino-acid distribution in DNA," Chaos, Solitons & Fractals, Elsevier, vol. 23(5), pages 1795-1807.
    Full references (including those not matched with items on IDEAS)

    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. Ro, Wosuk & Kwon, Younghun, 2009. "1/f Noise analysis of songs in various genre of music," Chaos, Solitons & Fractals, Elsevier, vol. 42(4), pages 2305-2311.
    2. Kim, Jongkwang & Kim, Sowun & Lee, Kunsang & Kwon, Younghun, 2009. "Entropy analysis in yeast DNA," Chaos, Solitons & Fractals, Elsevier, vol. 39(4), pages 1565-1571.
    3. Bhan, Jaemi & Kim, Sowoon & Kim, Jongkwang & Kwon, Younghun & Yang, Sung-il & Lee, Kunsang, 2006. "Long-range correlations in Korean literary corpora," Chaos, Solitons & Fractals, Elsevier, vol. 29(1), pages 69-81.

    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:454:y:2016:i:c:p:117-128. 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.