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Parallelizing exact motif finding algorithms on multi-core

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Abstract

The motif finding problem is one of the important and challenging problems in bioinformatics. A variety of sequential algorithms have been proposed to find exact motifs, but the running time is still not suitable due to high computational complexity of finding motifs. In this paper we parallelize three efficient sequential algorithms which are HEPPMSprune, PMS5 and PMS6. We implement the algorithms on a Dual Quad-Core machine using openMP to measure the performance of each algorithm. Our experiment on simulated data show that: (1) the parallel PMS6 is faster than the other algorithms in case of challenging instances, while the parallel HEPPMSprune is faster than the other algorithms in most of solvable instances; (2) the scalability of parallel HEPPMSprune is linear for all instances, while the scalability of parallel PMS5 and PMS6 is linear in case of challenging instances only; (3) the memory used by HEPPMSprune is less than that of the other algorithms.

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Acknowledgments

Part of this publication was made possible by NPRP Grant No. 4-1454-1-233 from the Qatar National Research Fund (a member of Qatar Foundation). The statements made herein are solely the responsibility of the authors. The authors are grateful to Dr. S. Bandyopadhyay of the University of Florida for providing us the PMS5 and PMS6 codes and for assisting us with several aspects of these codes. The authors also thank Prof. S. Rajasekaran of the University of Connecticut for providing us with the source code of PMSprune. Finally, the authors would like to thank the anonymous referees for their helpful comments. The first submission of this publication was done before the first author attended KINDI Lab.

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Authors and Affiliations

  1. KINDI Lab for Computing Research, College of Engineering, Qatar University, Doha, Qatar

    Mostafa M. Abbas

  2. Department of Basic Sciences, Faculty of Engineering, Sinai University, El-Arish, Egypt

    Mostafa M. Abbas

  3. Computer Science and Software Engineering Department, College of Computer Science and Engineering, Hail University, Hail, Kingdom of Saudi Arabia

    Hazem M. Bahig

  4. Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt

    Hazem M. Bahig

  5. Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt

    Mohamed Abouelhoda

  6. Center for Informatics Sciences, Nile University, Giza, Egypt

    Mohamed Abouelhoda

  7. Department of Mathematics, Faculty of Science, Al-Azhar University, Cairo, Egypt

    M. M. Mohie-Eldin

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  1. Mostafa M. Abbas
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  2. Hazem M. Bahig
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  3. Mohamed Abouelhoda
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  4. M. M. Mohie-Eldin
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Correspondence to Hazem M. Bahig.

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Abbas, M.M., Bahig, H.M., Abouelhoda, M. et al. Parallelizing exact motif finding algorithms on multi-core. J Supercomput 69, 814–826 (2014). https://doi.org/10.1007/s11227-014-1180-3

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