NestMSA: a new multiple sequence alignment algorithm

Multiple sequence alignment (MSA) is a core problem in many applications. Various optimization algorithms such as genetic algorithm and particle swarm optimization (PSO) have been used to solve this problem, where all of them are adapted to work in the bioinformatics domain. This paper defines the MSA problem, suggests a novel MSA algorithm called ‘NestMSA’ and evaluates it in two domains: Web data extraction and removing different URLs with similar text (DUST). The suggested algorithm is inspired by the PSO optimization algorithm. It is not a generalization of a two-sequence alignment algorithm as it processes all the sequences at the same time. Therefore, it looks globally at the same time on all sequences. Different from other PSO-based alignment algorithms, swarm particles in the proposed NestMSA algorithm are nested inside the sequences and communicated together to align them. Therefore, global maximum is guaranteed in our algorithm. Furthermore, this work suggests a new objective function which both maximizes the number of matched characters and minimizes the number of gaps inserted in the sequences. The running time complexity and the efficiency of NestMSA are addressed in this paper. The experiments show an encouraging result as it outperforms the two approaches DCA and TEX in the Web data extraction domain (95% and 96% of recall and precision, respectively). Furthermore, it gives a high-performance result in the DUST domain (95%, 93% and 92% of recall, precision and SPS score, respectively).