Hardware designs for local alignment of protein sequences

GÖK M., Yilmaz C.

21st International Symposium on Computer and Information Sciences (ISCIS 2006), İstanbul, Turkey, 1 - 03 November 2006, vol.4263, pp.277-278 identifier identifier

  • Publication Type: Conference Paper / Full Text
  • Volume: 4263
  • City: İstanbul
  • Country: Turkey
  • Page Numbers: pp.277-278
  • Çukurova University Affiliated: Yes


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 %.