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Many database applications, such as sequence comparing, sequence searching, and sequence matching, etc, process large database sequences. we introduce a novel and efficient technique to improve the performance of database applications by using a Hybrid GPU/CPU platform. In particular, our technique solves the problem of the low efficiency resulting from running short-length sequences in a database on a GPU. To verify our technique, we applied it to the widely used Smith-Waterman algorithm. The experimental results show that our Hybrid GPU/CPU technique improves the average performance by a factor of 2.2, and improves the peak performance by a factor of 2.8 when compared to earlier implementations.