Abstract
Dynamic programming algorithms are widely used to find the optimal sequence alignment between any two DNA sequences. This paper presents an innovative technique to significantly reduce the computation time and memory space requirements of the traceback phase of the Smith-Waterman algorithm, together with a flexible and scalable hardware architecture to accelerate the overall procedure. The results obtained from an implementation using a Virtex-4 FPGA showed that the proposed technique is feasible and is able to provide a significant speedup. For the considered test sequences, a speedup of about 6000 was obtained.
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