Parallelizing partial digest problem on multicore system

Hazem M. Bahig, Mostafa Abbas, M. M. Mohie-Eldin

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

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.

Original languageEnglish
Title of host publicationBioinformatics and Biomedical Engineering - 5th International Work-Conference, IWBBIO 2017, Proceedings
PublisherSpringer Verlag
Pages95-104
Number of pages10
ISBN (Print)9783319561530
DOIs
Publication statusPublished - 1 Jan 2017
Event5th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2017 - Granada, Spain
Duration: 26 Apr 201728 Apr 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10209 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other5th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2017
CountrySpain
City Granada
Period26/4/1728/4/17

Fingerprint

Sequential Algorithm
Partial
Exponential time
Exact Algorithms
Parallel Algorithms
Fast Algorithm
Experimental Study
Fragment
Speedup
Efficient Algorithms
Restriction
Decrease
Parallel algorithms
DNA

Keywords

  • Multicore
  • Parallel algorithm
  • Partial digest problem
  • Scalability

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Bahig, H. M., Abbas, M., & Mohie-Eldin, M. M. (2017). Parallelizing partial digest problem on multicore system. In Bioinformatics and Biomedical Engineering - 5th International Work-Conference, IWBBIO 2017, Proceedings (pp. 95-104). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10209 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-56154-7_10

Parallelizing partial digest problem on multicore system. / Bahig, Hazem M.; Abbas, Mostafa; Mohie-Eldin, M. M.

Bioinformatics and Biomedical Engineering - 5th International Work-Conference, IWBBIO 2017, Proceedings. Springer Verlag, 2017. p. 95-104 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10209 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Bahig, HM, Abbas, M & Mohie-Eldin, MM 2017, Parallelizing partial digest problem on multicore system. in Bioinformatics and Biomedical Engineering - 5th International Work-Conference, IWBBIO 2017, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10209 LNCS, Springer Verlag, pp. 95-104, 5th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2017, Granada, Spain, 26/4/17. https://doi.org/10.1007/978-3-319-56154-7_10
Bahig HM, Abbas M, Mohie-Eldin MM. Parallelizing partial digest problem on multicore system. In Bioinformatics and Biomedical Engineering - 5th International Work-Conference, IWBBIO 2017, Proceedings. Springer Verlag. 2017. p. 95-104. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-56154-7_10
Bahig, Hazem M. ; Abbas, Mostafa ; Mohie-Eldin, M. M. / Parallelizing partial digest problem on multicore system. Bioinformatics and Biomedical Engineering - 5th International Work-Conference, IWBBIO 2017, Proceedings. Springer Verlag, 2017. pp. 95-104 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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