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Intelligent Systems and Applications pp 301–321Cite as

Maximising Overlap Score in DNA Sequence Assembly Problem by Stochastic Diffusion Search

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Part of the book series: Studies in Computational Intelligence ((SCI,volume 650))

Abstract

This paper introduces a novel study on the performance of Stochastic Diffusion Search (SDS)—a swarm intelligence algorithm—to address DNA sequence assembly problem. This is an NP-hard problem and one of the primary problems in computational molecular biology that requires optimisation methodologies to reconstruct the original DNA sequence. In this work, SDS algorithm is adapted for this purpose and several experiments are run in order to evaluate the performance of the presented technique over several frequently used benchmarks. Given the promising results of the newly proposed algorithm and its success in assembling the input fragments, its behaviour is further analysed, thus shedding light on the process through which the algorithm conducts the task. Additionally, the algorithm is applied to overlap score matrices which are generated from the raw input fragments; the algorithm optimises the overlap score matrices to find better results. In these experiments real-world data are used and the performance of SDS is compared with several other algorithms which are used by other researchers in the field, thus demonstrating its weaknesses and strengths in the experiments presented in the paper.

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Notes

  1. 1.

    In American English, 1 billion is equated to a thousand million (i.e. 1, 000, 000, 000).

  2. 2.

    The results of these algorithms, other than SDS, are borrowed from [2].

  3. 3.

    These issues are explained in Sect. 3.

  4. 4.

    The results of these algorithms, other than SDS, are borrowed from [14].

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Author information

Authors and Affiliations

  1. Department of Computer Science, Kristianstad University, S-291 88, Kristianstad, Sweden

    Fatimah Majid al-Rifaie

  2. Computing Department, Goldsmiths, University of London, London, SE14 6NW, UK

    Mohammad Majid al-Rifaie

Authors
  1. Fatimah Majid al-Rifaie
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  2. Mohammad Majid al-Rifaie
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Correspondence to Fatimah Majid al-Rifaie .

Editor information

Editors and Affiliations

  1. Faculty of Computing and Engineering, University of Ulster at Jordanstown, Newtownabbey, United Kingdom

    Yaxin Bi

  2. The Science and Information (SAI) Organization, Bradford, West Yorkshire, United Kingdom

    Supriya Kapoor

  3. The Science and Information (SAI) Organization, Bradford, West Yorkshire, United Kingdom

    Rahul Bhatia

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Majid al-Rifaie, F., Majid al-Rifaie, M. (2016). Maximising Overlap Score in DNA Sequence Assembly Problem by Stochastic Diffusion Search. In: Bi, Y., Kapoor, S., Bhatia, R. (eds) Intelligent Systems and Applications. Studies in Computational Intelligence, vol 650. Springer, Cham. https://doi.org/10.1007/978-3-319-33386-1_15

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  • DOI: https://doi.org/10.1007/978-3-319-33386-1_15

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-33384-7

  • Online ISBN: 978-3-319-33386-1

  • eBook Packages: EngineeringEngineering (R0)

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