A Smith-Waterman Systolic Cell

  • C. W. Yu
  • K. H. Kwong
  • K. H. Lee
  • P. H. W. Leong
Conference paper

DOI: 10.1007/978-3-540-45234-8_37

Part of the Lecture Notes in Computer Science book series (LNCS, volume 2778)
Cite this paper as:
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

Abstract

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.

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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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