Identification of DNA motif using particle swarm optimization technique

Khedr, Ahmed Y.

International Journal of Advanced and Applied Sciences

Int. j. adv. appl. sci.

EISSN: 2313-3724

Print ISSN: 2313-626X

Volume 4, Issue 6 (June 2017), Pages: 84-87

Title: Identification of DNA motif using particle swarm optimization technique

Author(s): Ahmed Y. Khedr ^{1, 2,}*

Affiliation(s):

¹College of Computer Science and Engineering, Hail University, Hail, Saudi Arabia
²College of Engineering, Al-Azhar University, Cairo, Egypt

https://doi.org/10.21833/ijaas.2017.06.012

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Abstract:

The process of discovering short recurring patterns in DNA called DNA motif. DNA motif is an important part to study the biological cell functions. The main challenging of DNA motif is the running time to identify the motif where it increases with the length of motif and the number of mutations. Particle swarm optimization (PSO) is one of the efficient techniques to find an approximate solution using global optimization technique. We propose a PSO algorithm to find DNA motif. The experimental study on artificial data shows that the running time of the proposed algorithm is faster than recent proposed algorithms. The proposed algorithm is also compared to voting and hybrid algorithms for performance measure. In addition, the accuracy of the proposed algorithm is 90%. Finally, we apply the proposed algorithm on real data includes PDR3, GAL4, MATalpha2, and MCB.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Keywords: Soft computing, Swarm, Motif, DNA, Optimization

Article History: Received 20 March 2017, Received in revised form 11 May 2017, Accepted 16 May 2017

Digital Object Identifier:

https://doi.org/10.21833/ijaas.2017.06.012

Citation:

Khedr AY (2017). Identification of DNA motif using particle swarm optimization technique. International Journal of Advanced and Applied Sciences, 4(6): 84-87

http://www.science-gate.com/IJAAS/V4I6/Khedr.html

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