IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0050506.html
   My bibliography  Save this article

Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

Author

Listed:
  • Evan Senter
  • Saad Sheikh
  • Ivan Dotu
  • Yann Ponty
  • Peter Clote

Abstract

Using complex roots of unity and the Fast Fourier Transform, we design a new thermodynamics-based algorithm, FFTbor, that computes the Boltzmann probability that secondary structures differ by base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time and quadratic space , is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/.

Suggested Citation

  • Evan Senter & Saad Sheikh & Ivan Dotu & Yann Ponty & Peter Clote, 2012. "Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-13, December.
    • Handle: RePEc:plo:pone00:0050506
    DOI: 10.1371/journal.pone.0050506
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050506
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0050506&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0050506?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
    ---><---

    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:plo:pone00:0050506. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.