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Maximising overlap score in DNA sequence assembly problem by Stochastic Diffusion Search

al-Rifaie, Fatimah Majid and al-Rifaie, Mohammad Majid. 2016. Maximising overlap score in DNA sequence assembly problem by Stochastic Diffusion Search. In: , ed. Studies in Computational Intelligence. 650 Cham: Springer, pp. 301-321. ISBN 978-3-319-33384-7 [Book Section]

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Abstract or Description

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.

Item Type:

Book Section

Identification Number (DOI):

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

Keywords:

Electrophoresis, Expense, Adenine, Cytosine, Alba

Departments, Centres and Research Units:

Computing

Dates:

DateEvent
1 July 2016Published Online

Item ID:

17244

Date Deposited:

21 Mar 2016 12:43

Last Modified:

11 Jul 2018 07:23

URI:

http://research.gold.ac.uk/id/eprint/17244

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