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Parallelizing Partial Digest Problem on Multicore System

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Bioinformatics and Biomedical Engineering (IWBBIO 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10209))

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Abstract

The partial digest problem, PDP, is one of the methods used in restriction mapping to characterize a fragment of DNA. The main challenge of PDP is the exponential time for the best exact sequential algorithm in the worst case. In this paper, we reduce the running time for generating the solution of PDP by designing an efficient parallel algorithm. The algorithm is based on parallelizing the fastest sequential algorithm for PDP. The experimental study on a multicore system shows that the running time of the proposed algorithm decreases with the number of processors increases. Also, the speedup achieved good scales with increase in the number of processors.

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Author information

Authors and Affiliations

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

    Hazem M. Bahig

  2. College of Computer Science and Engineering, Hail University, Hail, Kingdom of Saudi Arabia

    Hazem M. Bahig

  3. Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar

    Mostafa M. Abbas

  4. KINDI Center for Computing Research, College of Engineering, Qatar University, Doha, Qatar

    Mostafa M. Abbas

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

    M. M. Mohie-Eldin

Authors
  1. Hazem M. Bahig
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  2. Mostafa M. Abbas
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  3. M. M. Mohie-Eldin
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Corresponding author

Correspondence to Hazem M. Bahig .

Editor information

Editors and Affiliations

  1. Universidad de Granada, Granada, Spain

    Ignacio Rojas

  2. Universidad de Granada, Granada, Spain

    Francisco Ortuño

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Bahig, H.M., Abbas, M.M., Mohie-Eldin, M.M. (2017). Parallelizing Partial Digest Problem on Multicore System. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science(), vol 10209. Springer, Cham. https://doi.org/10.1007/978-3-319-56154-7_10

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  • DOI: https://doi.org/10.1007/978-3-319-56154-7_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-56153-0

  • Online ISBN: 978-3-319-56154-7

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