Advertisement

Needleman–Wunsch Algorithm Using Multi-threading Approach

  • Sai Reetika PerumallaEmail author
  • Hemalatha Eedi
Conference paper
  • 17 Downloads
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 1090)

Abstract

Needleman–Wunsch algorithm (NWA) is one of the most popular algorithms in the area of bioinformatics to perform pair-wise sequence alignment. It uses dynamic programming to calculate the overall alignment score of two biological sequences. Using multithreading, this algorithm can be parallelized to achieve higher efficiency in terms of speed without compromising on the overall accuracy of the alignment. Multithreading can be implemented in multiple ways on the Needleman–Wunsch algorithm, each of which having different efficiencies in terms of speed and accuracy. The optimal number of threads for varying sequence lengths can also be identified using the results of the experiments performed.

Keywords

Sequence alignment Parallelization Needleman–Wunsch algorithm Multi-threading 

References

  1. 1.
    Mount, D.M. 2001. Bioinformatics: Sequence and Genome Analysis, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN 0-87969-608-7.Google Scholar
  2. 2.
  3. 3.
    Performance Improvement Of Genetic Algorithm For Multiple Sequence Alignment By Anderson Rici Amorim, JoaMatheusVerdadeiroVisotaky, Allan De GodoiContessoto Leandro Alves Neves, Roge ŕ ia Cristiane Grata De Souza, Carlos Roberto ValeˆNcio, Geraldo Francisco Donega ́ Zafalon.Google Scholar
  4. 4.
    Martins, W.S., J.B. Del Cuvillo, F.J. Useche, K.B.Theobald, and G.R. Gao. 2001. A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm For Sequence Comparison.Google Scholar
  5. 5.
    Nirmala Devi, S., and S.P. Rajagopalam. 2012. A Modified Dynamic Parallel Algorithm for Sequence Alignment in Biosequences.Google Scholar
  6. 6.
    Nemirovsky, M., and D.M. Tullsen. 2013. Multithreading Architecture. San Rafael: Morgan & Claypool.CrossRefGoogle Scholar
  7. 7.
    National Centre for Biotechnology Information. https://www.ncbi.nlm.nih.gov/.
  8. 8.
    Roberts, R. J. 2016. Nucleic Acid. Retrieved from https://www.britannica.com/science/nucleic-acid.
  9. 9.
  10. 10.
    Needleman, S.B., C.D. Wunsch. 1970. Needleman-Wunsch Algorithm for Sequence Similarity Searches. Journal of Molecular Biology 48: 443–453.Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  1. 1.Department of Computer ScienceJawaharlal Nehru Technological UniversityHyderabadIndia

Personalised recommendations