IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v391y2012i4p1255-1269.html
   My bibliography  Save this article

Evidence of codon usage in the nearest neighbor spacing distribution of bases in bacterial genomes

Author

Listed:
  • Higareda, M.F.
  • Geiger, O.
  • Mendoza, L.
  • Méndez-Sánchez, R.A.

Abstract

Statistical analysis of whole genomic sequences usually assumes a homogeneous nucleotide density throughout the genome, an assumption that has been proved incorrect for several organisms since the nucleotide density is only locally homogeneous. To avoid giving a single numerical value to this variable property, we propose the use of spectral statistics, which characterizes the density of nucleotides as a function of its position in the genome. We show that the cumulative density of bases in bacterial genomes can be separated into an average (or secular) plus a fluctuating part. Bacterial genomes can be divided into two groups according to the qualitative description of their secular part: linear and piecewise linear. These two groups of genomes show different properties when their nucleotide spacing distribution is studied. In order to analyze genomes having a variable nucleotide density, statistically, the use of unfolding is necessary, i.e., to get a separation between the secular part and the fluctuations. The unfolding allows an adequate comparison with the statistical properties of other genomes. With this methodology, four genomes were analyzed Burkholderia, Bacillus, Clostridium and Corynebacterium. Interestingly, the nearest neighbor spacing distributions or detrended distance distributions are very similar for species within the same genus but they are very different for species from different genera. This difference can be attributed to the difference in the codon usage.

Suggested Citation

  • Higareda, M.F. & Geiger, O. & Mendoza, L. & Méndez-Sánchez, R.A., 2012. "Evidence of codon usage in the nearest neighbor spacing distribution of bases in bacterial genomes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(4), pages 1255-1269.
    • Handle: RePEc:eee:phsmap:v:391:y:2012:i:4:p:1255-1269
    DOI: 10.1016/j.physa.2011.10.035
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437111008338
    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.2011.10.035?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. Jan Vegelius & Svante Janson & Folke Johansson, 1986. "Measures of similarity between distributions," Quality & Quantity: International Journal of Methodology, Springer, vol. 20(4), pages 437-441, December.
    2. José, Marco V. & Govezensky, Tzipe & Bobadilla, Juan R., 2005. "Statistical properties of DNA sequences revisited: the role of inverse bilateral symmetry in bacterial chromosomes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 351(2), pages 477-498.
    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. Yu Liu & Chaogui Kang & Song Gao & Yu Xiao & Yuan Tian, 2012. "Understanding intra-urban trip patterns from taxi trajectory data," Journal of Geographical Systems, Springer, vol. 14(4), pages 463-483, October.
    2. Kristoufek, Ladislav, 2012. "How are rescaled range analyses affected by different memory and distributional properties? A Monte Carlo study," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(17), pages 4252-4260.
    3. Kang, Chaogui & Ma, Xiujun & Tong, Daoqin & Liu, Yu, 2012. "Intra-urban human mobility patterns: An urban morphology perspective," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(4), pages 1702-1717.
    4. Suvorova Yulia M. & Korotkov Eugene V., 2015. "Study of triplet periodicity differences inside and between genomes," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(2), pages 113-123, April.

    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:391:y:2012:i:4:p:1255-1269. 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.