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PMS: A Panoptic Motif Search Tool

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  • Hieu Dinh
  • Sanguthevar Rajasekaran

Abstract

Background: Identification of DNA/Protein motifs is a crucial problem for biologists. Computational techniques could be of great help in this identification. In this direction, many computational models for motifs have been proposed in the literature. Methods: One such important model is the motif model. In this paper we describe a motif search web tool that predominantly employs this motif model. This web tool exploits the state-of-the art algorithms for solving the motif search problem. Results: The online tool has been helping scientists identify many unknown motifs. Many of our predictions have been successfully verified as well. We hope that this paper will expose this crucial tool to many more scientists. Availability and requirements: Project name: PMS - Panoptic Motif Search Tool. Project home page: http://pms.engr.uconn.edu or http://motifsearch.com. Licence: PMS tools will be readily available to any scientist wishing to use it for non-commercial purposes, without restrictions. The online tool is freely available without login.

Suggested Citation

  • Hieu Dinh & Sanguthevar Rajasekaran, 2013. "PMS: A Panoptic Motif Search Tool," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-7, December.
    • Handle: RePEc:plo:pone00:0080660
    DOI: 10.1371/journal.pone.0080660
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    References listed on IDEAS

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    1. Richard J Edwards & Norman E Davey & Denis C Shields, 2007. "SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins," PLOS ONE, Public Library of Science, vol. 2(10), pages 1-11, October.
    2. Hieu Dinh & Sanguthevar Rajasekaran & Jaime Davila, 2012. "qPMS7: A Fast Algorithm for Finding (ℓ, d)-Motifs in DNA and Protein Sequences," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-8, July.
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