IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0198922.html
   My bibliography  Save this article

Fast sequence analysis based on diamond sampling

Author

Listed:
  • Liangxin Gao
  • Wenzhen Bao
  • Hongbo Zhang
  • Chang-An Yuan
  • De-Shuang Huang

Abstract

Both in DNA and protein contexts, an important method for modelling motifs is to utilize position weight matrix (PWM) in biological sequences. With the development of genome sequencing technology, the quantity of the sequence data is increasing explosively, so the faster searching algorithms which have the ability to meet the increasingly need are desired to develop. In this paper, we proposed a method for speeding up the searching process of candidate transcription factor binding sites (TFBS), and the users can be allowed to specify p threshold to get the desired trade-off between speed and sensitivity for a particular sequence analysis. Moreover, the proposed method can also be generalized to large-scale annotation and sequence projects.

Suggested Citation

  • Liangxin Gao & Wenzhen Bao & Hongbo Zhang & Chang-An Yuan & De-Shuang Huang, 2018. "Fast sequence analysis based on diamond sampling," PLOS ONE, Public Library of Science, vol. 13(6), pages 1-14, June.
    • Handle: RePEc:plo:pone00:0198922
    DOI: 10.1371/journal.pone.0198922
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198922
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0198922&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0198922?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:pone00:0198922. 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.