IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v14y2015i2p113-123n1.html
   My bibliography  Save this article

Study of triplet periodicity differences inside and between genomes

Author

Listed:
  • Suvorova Yulia M.

    (Bioinformatics Laboratory, Centre of Bioengineering of the Russian Academy of Sciences, 117312, Prospect 60-tya Oktyabrya, Moscow, Russian Federation)

  • Korotkov Eugene V.

Abstract

Triplet periodicity (TP) is a distinctive feature of the protein coding sequences of both prokaryotic and eukaryotic genomes. In this work, we explored the TP difference inside and between 45 prokaryotic genomes. We constructed two hypotheses of TP distribution on a set of coding sequences and generated artificial datasets that correspond to the hypotheses. We found that TP is more similar inside a genome than between genomes and that TP distribution inside a real genome dataset corresponds to the hypothesis which implies that a common TP pattern exists for the majority of sequences inside a genome. Additionally, we performed gene classification based on TP matrixes. This classification showed that TP allows identification of the genome to which a given gene belongs with more than 85% accuracy.

Suggested Citation

  • 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.
    • Handle: RePEc:bpj:sagmbi:v:14:y:2015:i:2:p:113-123:n:1
    DOI: 10.1515/sagmb-2013-0063
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2013-0063
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2013-0063?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. Jon Bohlin & Eystein Skjerve, 2009. "Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-12, 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. Jon Bohlin & Ola Brynildsrud & Tammi Vesth & Eystein Skjerve & David W Ussery, 2013. "Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-10, July.
    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. 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.

    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:bpj:sagmbi:v:14:y:2015:i:2:p:113-123:n:1. 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    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.