PHGA-COFFEE: Aligning Multiple Sequences by Parallel Hybrid Genetic Algorithm
Liu Li · Chinese Journal of Computers · 2006
A parallel hybrid genetic algorithm and an associated software package called PHGA-COFFEE are presented. The COFFEE function is used to measure individual fitness, and six genetic operators are designed, especially two novel mutation operators are proposed, one is designed based on the COFFEE's consistency information that can improve the global search ability, and another is realized by dynamic programming method that can improve individuals locally. Experimental results of the 144 benchmarks from the BAliBASE show that the proposed algorithm is feasible, and for datasets in twilight zone and comprising N/C terminal extensions, PHGA-COFFEE generates better alignment as compared to other methods. At the same time, the computation time of PHGA-COFFEE is remarkably reduced due to the parallel algorithm.