An Efficient PSO-Based Algorithm for Finding Maximal Exact Match in Large DNA Sequences

Abstract

With the appearance of complete mammalian genomes, comparative approaches have experienced a recent upsurge. Searching maximal exact match is among the most used tasks in sequence searching within a larger DNA sequence or database. Many exact algorithms have been designed to deal with this problem. The best improvements made by these algorithms have led to a time and space complexity of O(n) and they remain practically less effective for large sequences. Heuristic methods will therefore be a good alternative to implement. In this work, we present an efficient heuristic algorithm based on PSO metaheuristic to deal with the problem of searching the maximal exact match of small searched sequences in large ones. The time and space complexity of the designed algorithm is of O(1). The experimental results showed the efficiency of the proposed search algorithm for finding maximal exact match in large sequences when compared with two other sequence searching algorithms.