A simulated annealing algorithm for multiple sequence alignment with guaranteed accuracy

For multiple sequence alignment problem in molecular biological sequence analysis, when input sequence number is very large, many heuristic algorithms have been proposed to improve the computation speed and the quality of alignment. We present a novel algorithm SASAlign for multiple sequence alignment. This can guarantee that the multiple alignment obtained from the SASAlign is within a factor of two from the optimal multiple sequence alignment. Experimental results show that the proposed algorithm is feasible, as the SASAlign algorithm outperforms the HMMT and SA for most of the cases and is competitive with the other methods, such as ClustalW, SAGA, MultAlign, and DiAlign.