IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v6y2007i1n22.html
   My bibliography  Save this article

H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps

Author

Listed:
  • Fayyaz movaghar Afshin

    (Institute of Mathematics of Toulouse, University Toulouse 2)

  • Mercier Sabine

    (Institute of Mathematics of Toulouse, University Toulouse 2)

  • Ferré Louis

    (Institute of Mathematics of Toulouse, University Toulouse 2)

Abstract

We propose an approximate distribution for the gapped local score of a two sequence comparison. Our method stands on combining an adapted scoring scheme that includes the gaps and an approximate distribution of the ungapped local score of two independent sequences of i.i.d. random variables. The new scoring scheme is defined on h-tuples of the sequences, using the gapped global score. The influence of h and the accuracy of the p-value are numerically studied and compared with obtained p-value of BLAST. The numerical experiments emphasize that our approximate p-values outperform the BLAST ones, particularly for both simulated and real short sequences.

Suggested Citation

  • Fayyaz movaghar Afshin & Mercier Sabine & Ferré Louis, 2007. "H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 6(1), pages 1-21, August.
    • Handle: RePEc:bpj:sagmbi:v:6:y:2007:i:1:n:22
    DOI: 10.2202/1544-6115.1272
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1272
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.2202/1544-6115.1272?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

    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:6:y:2007:i:1:n:22. 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: 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.