A new algorithm for solving sequence alignment problem is proposed, which is named SAPS (Simulated Annealing with Previous Solutions). This algorithm is based on the classical Simulated Annealing (SA). SAPS is implemented in order to obtain results of pair and multiple sequence alignment. SA is a simulation of heating and cooling of a metal to solve an optimization problem. In order to select randomly a current solution, SAPS algorithm chooses a solution from solutions that have been previously generated within the Metropolis Cycle. This simple change has led to increase the quality of the solution to the problem of aligning genomic sequences with respect to the classical Simulated Annealing algorithm. The parameters of SAPS, for certain instances, are tuned by an analytical method, and some parameters have experimentally been tuned. SAPS has generated high-quality results in comparison with the classical SA. The instances used are specific genes of the AIDS virus.
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