We present a novel algorithm SASAlignSimulated annealing with star-alignment. In the SASAlign, instead of starting with an initial solution chosen at random, we use the results formed by star-alignment to give a good starting point as the initial solution to the SA for further refinement. The time required by the algorithm scales linearly with the number of sequences in S, linearly with the number of iterations, and cube with the length of the sequences, that is
). Experiments on the BAliBASE benchmark database also show that the proposed algorithm is efficient, and prove to be competitive with and better than the other method HMMT.