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Parallelizing Partial Digest Problem on Multicore System

Conference paper
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Part of the Lecture Notes in Computer Science book series (LNCS, volume 10209)

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.

Keywords

Partial digest problem Parallel algorithm Scalability Multicore 

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.Computer Science Division, Department of Mathematics, Faculty of ScienceAin Shams UniversityCairoEgypt
  2. 2.College of Computer Science and EngineeringHail UniversityHailKingdom of Saudi Arabia
  3. 3.Qatar Computing Research InstituteHamad Bin Khalifa UniversityDohaQatar
  4. 4.KINDI Center for Computing Research, College of EngineeringQatar UniversityDohaQatar
  5. 5.Department of Mathematics, Faculty of ScienceAl-Azhar UniversityCairoEgypt

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