Hardware Designs for Local Alignment of Protein Sequences

  • Mustafa Gök
  • Çağlar Yılmaz
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4263)


Local alignment of two protein sequences shows the similar regions between these proteins. Usually, a query protein sequence is aligned with several hundred thousands of protein sequences stored in databases. Since this procedure is computationally demanding, various hardware units are designed to get high quality results in a practically useful time. This paper presents efficient hardware designs that compute the local alignment scores of protein sequences. The presented designs are compared with the reference designs. All designs are implemented using ASIC and FPGA technologies. Syntheses results show that compared to the reference designs the proposed ASIC implementations achieve frequency improvements up to 250 % and hardware gains up to 40 %, and the proposed FPGA implementations achieve frequency improvements up to 29 % and hardware gains up to 48 %.


Local Alignment Systolic Array Hardware Design Reference Design FPGA Implementation 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Mustafa Gök
    • 1
  • Çağlar Yılmaz
    • 1
  1. 1.Dept. of Comp Eng. BalcaliCukurova UniversityTurkey

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