Parallelizing Partial Digest Problem on Multicore System

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


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.


Partial digest problem Parallel algorithm Scalability Multicore 


  1. 1.
    Pevzner, P.: DNA physical mapping and alternating eulerian cycles in colored graphs. Algorithmica 13(1–2), 77–105 (1995)CrossRefzbMATHMathSciNetGoogle Scholar
  2. 2.
    Devine, J.H., Kutuzova, G.D., Green, V.A., Ugarova, N.N., Baldwin, T.O.: Luciferase from the east European firefly Luciola mingrelica: cloning and nucleotide sequence of the cDNA, overexpression in Escherichia coli and purification of the enzyme. Biochimica et Biophysica Acta (BBA)-Gene Struct. Expr. 1173(2), 121–132 (1993)Google Scholar
  3. 3.
    Baker, M.: Gene-editing nucleases. Nat. Methods 9(1), 23–26 (2012)CrossRefGoogle Scholar
  4. 4.
    Sambrook, J., Fritsch, E.F., Maniatis, T.: Molecular Cloning. A Laboratory Manual, 2nd edn., pp. 1.63–1.70. Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989)Google Scholar
  5. 5.
    He, X., Hull, V., Thomas, J.A., Fu, X., Gidwani, S., Gupta, Y.K., Black, L.W., Xu, S.Y.: Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference. Sci. Rep. 5, 9747 (2015)Google Scholar
  6. 6.
    Narayanan, P.: Bioinformatics: A Primer. New Age International (2005)Google Scholar
  7. 7.
    Dear, P.H.: Genome mapping. eLS (2001)Google Scholar
  8. 8.
    Jones, N.C., Pevzner, P.: An Introduction to Bioinformatics Algorithms. MIT Press, Cambridge (2004)Google Scholar
  9. 9.
    Lemke, P., Werman, M.: On the complexity of inverting the autocorrelation function of a finite integer sequence, and the problem of locating n points on a line, given the (nC2) unlabelled distances between them. Preprint 453 (1988)Google Scholar
  10. 10.
    Daurat, A., Gérard, Y., Nivat, M.: Some necessary clarifications about the chords’ problem and the partial digest problem. Theoret. Comput. Sci. 347(1–2), 432–436 (2005)CrossRefzbMATHMathSciNetGoogle Scholar
  11. 11.
    Cieliebak, M., Eidenbenz, S., Penna, P.: Noisy Data Make the Partial Digest Problem NP-Hard. Springer, Heidelberg (2003)CrossRefzbMATHGoogle Scholar
  12. 12.
    Pandurangan, G., Ramesh, H.: The restriction mapping problem revisited. J. Comput. Syst. Sci. 65(3), 526–544 (2002)CrossRefzbMATHMathSciNetGoogle Scholar
  13. 13.
    Błażewicz, J., Formanowicz, P., Kasprzak, M., Jaroszewski, M., Markiewicz, W.T.: Construction of DNA restriction maps based on a simplified experiment. Bioinformatics 17(5), 398–404 (2001)CrossRefGoogle Scholar
  14. 14.
    Blazewicz, J., Burke, E.K., Kasprzak, M., Kovalev, A., Kovalyov, M.Y.: Simplified partial digest problem: enumerative and dynamic programming algorithms. IEEE/ACM Trans. Comput. Biol. Bioinf. 4(4), 668–680 (2007)CrossRefGoogle Scholar
  15. 15.
    Karp, R.M., Newberg, L.A.: An algorithm for analysing probed partial digestion experiments. Comput. Appl. Biosci. 11(3), 229–235 (1995)Google Scholar
  16. 16.
    Nadimi, R., Fathabadi, H.S., Ganjtabesh, M.: A fast algorithm for the partial digest problem. Jpn J. Ind. Appl. Math. 28(2), 315–325 (2011)CrossRefzbMATHMathSciNetGoogle Scholar
  17. 17.
    Ahrabian, H., Ganjtabesh, M., Nowzari-Dalini, A., Razaghi-Moghadam-Kashani, Z.: Genetic algorithm solution for partial digest problem. Int. J. Bioinform. Res. Appl. 9(6), 584–594 (2013)CrossRefGoogle Scholar
  18. 18.
    Skiena, S.S., Smith, W.D., Lemke, P.: Reconstructing sets from interpoint distances. In: Proceedings of the Sixth Annual Symposium on Computational Geometry, pp. 332–339. ACM (1990)Google Scholar
  19. 19.
    Fomin, E.: A simple approach to the reconstruction of a set of points from the multiset of n2 pairwise distances in n2 steps for the sequencing problem: II algoirthm. J. Comput. Biol. 23, 1–7 (2016)CrossRefMathSciNetGoogle Scholar
  20. 20.
    Abbas, M.M., Bahig, H.M.: A fast exact sequential algorithm for the partial digest problem. BMC Bioinform. 17, 1365 (2016)CrossRefGoogle Scholar
  21. 21.
    Zhang, Z.: An exponential example for a partial digest mapping algorithm. J. Comput. Biol. 1(3), 235–239 (1994)CrossRefGoogle Scholar

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

Personalised recommendations