This paper presents a new sequence alignment method using the divide approach, which solves the problem by decomposing sequence alignment into several sub-alignments with respect to exact matching subsequences. Exact matching subsequences in the proposed method are bounded on the generalized suffix tree of two sequences, such as protein domain length more than 7 and less than 7. Experiment results show that protein sequence pairs chosen in PFAM database can be aligned using this method. In addition, this method reduces the time about 15% and space of the conventional dynamic programming approach. And the sequences were classified with 94% of accuracy.