Abstract
Sequence alignment is one of the most important research content of bioinformatics. In this paper, a novel chaos particle swarm optimization algorithm which is adapting to solving sequence alignment problem was proposed. In this method, particle swarm optimization algorithm was improved for aiming at the characteristics of the problem of solving sequence alignment and using chaos searching to avoid local convergence enhancing the ability of global convergence. The experiments show that the alignment results of proposed method excels basic PSO and avoiding prematurity of basic PSO. The proposed method can get better alignment results in DNA and protein sequences and is efficient and feasible, getting best results especially in the sequences of medium or short length.
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