Large Scale Protein Sequence Alignment Using FPGA Reprogrammable Logic Devices

  • Stefan Dydel
  • Piotr Bała
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3203)


In this paper we show how to significantly accelerate Smith-Waterman protein sequence alignment algorithm using reprogrammable logic devices – FPGAs (Field Programmable Gate Array). Due to perfect sensitivity, the Smith-Waterman algorithm is important in a field of computational biology but computational complexity makes it impractical for large database searches when running on general purpose computers.

Current approach allows for aminoacid sequence alignment with full substitution matrix which leads to more complex formula than used in DNA alignment and is much more memory demanding. We propose different parellization scheme than commonly used systolic arrays, leading to full utilization of PUs (Processing Units), regardless of sequence length. FPGA based implementation of Smith-Waterman algorithm can accelerate sequence alignment on a Pentium desktop computer by two orders of magnitude comparing to standard OSEARCH program from FASTA package.


Field Programmable Gate Array Systolic Array Edit Operation Longe Common Subsequence General Purpose Computer 
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 2004

Authors and Affiliations

  • Stefan Dydel
    • 1
  • Piotr Bała
    • 1
  1. 1.Faculty of Mathematics and Computer ScienceN. Copernicus UniversityTorunPoland

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