DNA motif discovery using chemical reaction optimization

Abstract

DNA motif discovery means to find short similar sequence elements within a set of nucleotide sequences. It has become a compulsory need in bioinformatics for its useful applications such as compression, summarization, and clustering algorithms. Motif discovery is an NP-hard problem and exact algorithms cannot solve it in polynomial time. Many optimization algorithms were proposed to solve this problem. However, none of them can show its supremacy by overcoming all the obstacles. Chemical Reaction Optimization (CRO) is a population based metaheuristic algorithm that can easily fit for the optimization problem. Here, we have proposed an algorithm based on Chemical Reaction Optimization technique to solve the DNA motif discovery problem. The four basic operators of CRO have been redesigned for this problem to search the solution space locally as well as globally. Two additional operators (repair functions) have been proposed to improve the quality of the solutions. They have been applied to the final solution after the iteration stage of CRO to get a better one. Using the flexible mechanism of elementary operators of CRO along with the additional operators (repair functions), it is possible to determine motif more precisely. Our proposed method is compared with other traditional algorithms such as Gibbs sampler, AlignACE (Aligns Nucleic Acid Conserved Elements), MEME (Multiple Expectation Maximization for Motif Elicitation), and ACRI (Ant-Colony-Regulatory-Identification) by testing real-world datasets. The experimental results show that the proposed algorithm can give better results than other traditional algorithms in quality and in less running time. Besides, statistical tests have been performed to show the superiority of the proposed algorithm over other state-of-the-arts in this area.