article

Improved exact enumerative algorithms for the planted (l, d)-motif search problem

Author:

Shunji TanakaAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 11, Issue 2

Pages 361 - 374

https://doi.org/10.1109/TCBB.2014.2306842

Published: 01 March 2014 Publication History

Abstract

In this paper efficient exact algorithms are proposed for the planted (l, d)-motif search problem. This problem is to find all motifs of length l that are planted in each input string with at most d mismatches. The "quorum" version of this problem is also treated in this paper to find motifs planted not in all input strings but in at least q input strings. The proposed algorithms are based on the previous algorithms called qPMSPruneI and qPMS7 that traverse a search tree starting from a l-length substring of an input string. To improve these previous algorithms, several techniques are introduced, which contribute to reducing the computation time for the traversal. In computational experiments, it will be shown that the proposed algorithms outperform the previous algorithms.

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Cited By

Theepalakshmi PReddy U(2024)A new efficient quorum planted (ℓ, d) motif search on ChIP-seq dataset using segmentation to filtration and freezing firefly algorithmsSoft Computing - A Fusion of Foundations, Methodologies and Applications10.1007/s00500-023-09236-z28:4(3049-3070)Online publication date: 1-Feb-2024
https://dl.acm.org/doi/10.1007/s00500-023-09236-z
(2018)Randomised sequential and parallel algorithms for efficient quorum planted motif searchInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2017.08645718:2(105-124)Online publication date: 23-Dec-2018
https://dl.acm.org/doi/10.1504/IJDMB.2017.086457
Kazemian FFazlali MKatanforoush ARezvani M(2018)Parallel implementation of quorum planted (, d) motif search on multi-core/many-core platformsMicroprocessors & Microsystems10.1016/j.micpro.2016.06.00846:PB(255-263)Online publication date: 28-Dec-2018
https://dl.acm.org/doi/10.1016/j.micpro.2016.06.008
Show More Cited By

Index Terms

Improved exact enumerative algorithms for the planted (l, d)-motif search problem
1. Applied computing
  1. Life and medical sciences
2. Theory of computation
  1. Design and analysis of algorithms
  2. Theory and algorithms for application domains
    1. Machine learning theory
      1. Reinforcement learning
        Sequential decision making

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Information & Contributors

Information

Published In

cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 11, Issue 2

March/April 2014

160 pages

ISSN:1545-5963

Editor:
Ying Xu

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Publisher

IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 March 2014

Accepted: 07 February 2014

Revised: 06 January 2014

Received: 27 May 2013

Published in TCBB Volume 11, Issue 2

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Cited By

Theepalakshmi PReddy U(2024)A new efficient quorum planted (ℓ, d) motif search on ChIP-seq dataset using segmentation to filtration and freezing firefly algorithmsSoft Computing - A Fusion of Foundations, Methodologies and Applications10.1007/s00500-023-09236-z28:4(3049-3070)Online publication date: 1-Feb-2024
https://dl.acm.org/doi/10.1007/s00500-023-09236-z
(2018)Randomised sequential and parallel algorithms for efficient quorum planted motif searchInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2017.08645718:2(105-124)Online publication date: 23-Dec-2018
https://dl.acm.org/doi/10.1504/IJDMB.2017.086457
Kazemian FFazlali MKatanforoush ARezvani M(2018)Parallel implementation of quorum planted (, d) motif search on multi-core/many-core platformsMicroprocessors & Microsystems10.1016/j.micpro.2016.06.00846:PB(255-263)Online publication date: 28-Dec-2018
https://dl.acm.org/doi/10.1016/j.micpro.2016.06.008
Zhang JWang YZhang CShi Y(2016)Mining Contiguous Sequential Generators in Biological SequencesIEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)10.1109/TCBB.2015.249513213:5(855-867)Online publication date: 1-Sep-2016
https://dl.acm.org/doi/10.1109/TCBB.2015.2495132

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