Yu C.W., Kwong K.H., Lee K.H., Leong P.H.W. (2003) A Smith-Waterman Systolic Cell. In: Y. K. Cheung P., Constantinides G.A. (eds) Field Programmable Logic and Application. FPL 2003. Lecture Notes in Computer Science, vol 2778. Springer, Berlin, Heidelberg
With an aim to understand the information encoded by DNA sequences, databases containing large amount of DNA sequence information are frequently compared and searched for matching or near-matching patterns. This kind of similarity calculation is known as sequence alignment. To date, the most popular algorithms for this operation are heuristic approaches such as BLAST and FASTA which give high speed but low sensitivity, i.e. significant matches may be missed by the searches. Another algorithm, the Smith-Waterman algorithm, is a more computationally expensive algorithm but achieves higher sensitivity. In this paper, an improved systolic processing element cell for implementing the Smith-Waterman on a Xilinx Virtex FPGA is presented.