Computational Biology and Bioinformatics

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A New Idea for Improving the Running Time of PMS Algorithm

Received: 03 May 2016    Accepted: 16 May 2016    Published: 28 May 2016
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Abstract

Motif finding problem is a major challenge in biology with significant applications in the detection of transcription factor binding sites and transcriptional regulatory elements that are crucial in understanding gene expression and function, human disease, drug design, etc. Two type of motif finding problems have been investigated. Planted Motif Search Problem (PMSP) which is defined as finding motifs that appear in all sequences and a restricted version of it “Planted Motif Search Problem-Sample Driven” (PMSP-SD) where the motifs themselves are found in the input. The first version is NP-Complete and the second version can be trivially solved in polynomial time. In this paper, a new idea is used to speed up the PMS-SD algorithm. Although PMS-SD is a polynomial time algorithm and the new idea does not improve its asymptotic runtime, but since most of the motif search algorithms combine a sample driven approach with a pattern driven approach, the speed up of PMS-SD running time would result in speed up of PMS algorithm. To verify the performance of the modified algorithms which are called PMS-two step and PMS-SD-two step, these algorithms are tested on simulated data. The experimental results approve the improvements.

DOI 10.11648/j.cbb.20160402.11
Published in Computational Biology and Bioinformatics (Volume 4, Issue 2, April 2016)
Page(s) 15-20
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Pattern and Motif Discovery, Planted (l,d)-Motif Search Problem, Closest Substring Problem

References
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Author Information
  • Department of Applied Mathematics, Faculty of Mathematical Science, University of Guilan, Rasht, Iran

  • Department of Applied Mathematics, Faculty of Mathematical Science, University of Guilan, Rasht, Iran

  • Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran

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  • APA Style

    Saeed Alirezanejad Gohardani, Mehri Bagherian, Hamid Reza Vaziri. (2016). A New Idea for Improving the Running Time of PMS Algorithm. Computational Biology and Bioinformatics, 4(2), 15-20. https://doi.org/10.11648/j.cbb.20160402.11

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    ACS Style

    Saeed Alirezanejad Gohardani; Mehri Bagherian; Hamid Reza Vaziri. A New Idea for Improving the Running Time of PMS Algorithm. Comput. Biol. Bioinform. 2016, 4(2), 15-20. doi: 10.11648/j.cbb.20160402.11

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    AMA Style

    Saeed Alirezanejad Gohardani, Mehri Bagherian, Hamid Reza Vaziri. A New Idea for Improving the Running Time of PMS Algorithm. Comput Biol Bioinform. 2016;4(2):15-20. doi: 10.11648/j.cbb.20160402.11

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  • @article{10.11648/j.cbb.20160402.11,
      author = {Saeed Alirezanejad Gohardani and Mehri Bagherian and Hamid Reza Vaziri},
      title = {A New Idea for Improving the Running Time of PMS Algorithm},
      journal = {Computational Biology and Bioinformatics},
      volume = {4},
      number = {2},
      pages = {15-20},
      doi = {10.11648/j.cbb.20160402.11},
      url = {https://doi.org/10.11648/j.cbb.20160402.11},
      eprint = {https://download.sciencepg.com/pdf/10.11648.j.cbb.20160402.11},
      abstract = {Motif finding problem is a major challenge in biology with significant applications in the detection of transcription factor binding sites and transcriptional regulatory elements that are crucial in understanding gene expression and function, human disease, drug design, etc. Two type of motif finding problems have been investigated. Planted Motif Search Problem (PMSP) which is defined as finding motifs that appear in all sequences and a restricted version of it “Planted Motif Search Problem-Sample Driven” (PMSP-SD) where the motifs themselves are found in the input. The first version is NP-Complete and the second version can be trivially solved in polynomial time. In this paper, a new idea is used to speed up the PMS-SD algorithm. Although PMS-SD is a polynomial time algorithm and the new idea does not improve its asymptotic runtime, but since most of the motif search algorithms combine a sample driven approach with a pattern driven approach, the speed up of PMS-SD running time would result in speed up of PMS algorithm. To verify the performance of the modified algorithms which are called PMS-two step and PMS-SD-two step, these algorithms are tested on simulated data. The experimental results approve the improvements.},
     year = {2016}
    }
    

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  • TY  - JOUR
    T1  - A New Idea for Improving the Running Time of PMS Algorithm
    AU  - Saeed Alirezanejad Gohardani
    AU  - Mehri Bagherian
    AU  - Hamid Reza Vaziri
    Y1  - 2016/05/28
    PY  - 2016
    N1  - https://doi.org/10.11648/j.cbb.20160402.11
    DO  - 10.11648/j.cbb.20160402.11
    T2  - Computational Biology and Bioinformatics
    JF  - Computational Biology and Bioinformatics
    JO  - Computational Biology and Bioinformatics
    SP  - 15
    EP  - 20
    PB  - Science Publishing Group
    SN  - 2330-8281
    UR  - https://doi.org/10.11648/j.cbb.20160402.11
    AB  - Motif finding problem is a major challenge in biology with significant applications in the detection of transcription factor binding sites and transcriptional regulatory elements that are crucial in understanding gene expression and function, human disease, drug design, etc. Two type of motif finding problems have been investigated. Planted Motif Search Problem (PMSP) which is defined as finding motifs that appear in all sequences and a restricted version of it “Planted Motif Search Problem-Sample Driven” (PMSP-SD) where the motifs themselves are found in the input. The first version is NP-Complete and the second version can be trivially solved in polynomial time. In this paper, a new idea is used to speed up the PMS-SD algorithm. Although PMS-SD is a polynomial time algorithm and the new idea does not improve its asymptotic runtime, but since most of the motif search algorithms combine a sample driven approach with a pattern driven approach, the speed up of PMS-SD running time would result in speed up of PMS algorithm. To verify the performance of the modified algorithms which are called PMS-two step and PMS-SD-two step, these algorithms are tested on simulated data. The experimental results approve the improvements.
    VL  - 4
    IS  - 2
    ER  - 

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