Efficient cell designs for systolic Smith-Waterman implementations

GÖK M., Yilmaz C.

16th International Conference on Field Programmable Logic and Applications, Madrid, Spain, 28 - 30 August 2006, pp.889-892 identifier identifier

  • Publication Type: Conference Paper / Full Text
  • Volume:
  • Doi Number: 10.1109/fpl.2006.311337
  • City: Madrid
  • Country: Spain
  • Page Numbers: pp.889-892
  • Çukurova University Affiliated: Yes


Smith-Waterman algorithm is used to search bioinformatics databases. The systolic array implementations of this algorithm can search databases hundreds of times faster than software applications. The performances of the systolic Smith-Waterman implementations mainly depend on the number of cells they contain and the clock frequencies of the cells. This paper presents efficient cell designs for systolic Smith-Waterman implementations. The designs that use the presented cells and the recent reference designs are mapped on the same FPGA platform and compared by syntheses. Syntheses results show that the performance of the presented designs are 1.7 to 3.6 times higher than the reference designs.