Multiple Biological Sequence Alignment with a Parallel Island Injection Genetic Algorithm

Abstract

Multiple sequence alignment (MSA) is an important problem in Bioinformatics since it is often used to identify evolutionary relationships and predict secondary/tertiary structure, among others. MSAs are usually scored with the Sum-of-Pairs (SP) function and the exact SP MSA is known to be NP-Hard. Therefore, heuristic methods are used to solve this problem. In this paper, we propose and evaluate a parallel island injection genetic algorithm to solve the MSA problem. Unlike the other strategies, our parallel solution uses two types of interconnected archipelagoes, each with distinct types of individuals. Our results with real protein data sets show that our strategy is able to obtain better results, when compared to the traditional island model. Also, we were able to reduce considerably the execution time, when compared to the sequential version.