Title: EGSA: a new enhanced gravitational search algorithm to resolve multiple sequence alignment problem
Authors: Elamine Zemali; Abdelmadjid Boukra
Addresses: Department of Computer Science, University of Science and Technologies Houari Boumedienne (USTHB), Bab Ezzouar, Algiers, Algeria ' Department of Computer Science, University of Science and Technologies Houari Boumedienne (USTHB), Bab Ezzouar, Algiers, Algeria
Abstract: Multiple sequence alignment is a very important and useful tool for genomic analysis in many tasks in bioinformatics. However, finding an accurate alignment of DNA or protein sequences is very difficult since the computational effort required grows exponentially with the sequences number. In this paper, we propose a new sequence alignment algorithm based on gravitational search algorithm (GSA). The gravitational search algorithm (GSA) is a recent metaheuristic inspired from Newton's laws of universal gravitation and motion. Moreover, to avoid the convergence toward local optima, we enhance GSA behaviour by introducing a new mechanism based on simulated annealing concept. Such concept offers a good balance between the exploration and exploitation in GSA and can lead to good alignment quality for the MSA problem. The accuracy and efficiency of the proposed algorithm are compared with recent and well-known alignment methods using BAliBASE benchmark database. The analysis of the experimental results shows that the algorithm can achieve competitive solutions quality.
Keywords: multiple sequence alignment; MSA; gravitational search algorithm; GSA; metaheuristics; bioinformatics; simulated annealing.
International Journal of Intelligent Engineering Informatics, 2018 Vol.6 No.1/2, pp.204 - 217
Received: 19 Nov 2016
Accepted: 22 May 2017
Published online: 02 Apr 2018 *