A Smith-Waterman Systolic Cell

  • C. W. Yu
  • K. H. Kwong
  • K. H. Lee
  • P. H. W. Leong
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2778)


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.


Processing Element Edit Distance Systolic Array FPGA Device Celera Genomic 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • C. W. Yu
    • 1
  • K. H. Kwong
    • 1
  • K. H. Lee
    • 1
  • P. H. W. Leong
    • 1
  1. 1.Department of Computer Science and EngineeringThe Chinese University of Hong KongShatin, New Territories, Hong Kong SARChina

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