C-Based Design Methodology for FPGA Implementation of ClustalW MSA

  • Yan Lin Aung
  • Douglas L. Maskell
  • Timothy F. Oliver
  • Bertil Schmidt
  • William Bong
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4774)


Systolisation of the pairwise distance computation algorithm and mapping into field programmable gate arrays (FPGA) have proven to give superior performance at a lower cost, compared to the same algorithm running on a cluster of workstations. The primary design methodology for this approach is based on the hardware description languages such as VHDL and Verilog HDL. An alternative design methodology, however, is the use of a high level language such as C to describe the algorithms and generate equivalent hardware descriptions for implementation in FPGA so as to reduce time to market. This paper describes the design and implementation of the ClustalW first stage multiple sequence alignment based on the Smith-Waterman algorithm on a low cost FPGA development platform using a C language development tool suite. Performance evaluation results show that comparable performance could be achieved to that of Pentium 4 systems and other HDL-based solutions using even the smallest commercially available FPGA device with this design methodology.


multiple sequence alignment ClustalW FPGA sequence analysis 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Yan Lin Aung
    • 1
  • Douglas L. Maskell
    • 1
  • Timothy F. Oliver
    • 1
  • Bertil Schmidt
    • 2
  • William Bong
    • 3
  1. 1.School of Computer Engineering, NTUSingapore
  2. 2.Division of Engineering, Science and Technology, UNSW AsiaSingapore
  3. 3.Network Storage Technology Division, A*STAR Data Storage InstituteSingapore

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