DocumentCode
2447581
Title
Fast Smith-Waterman hardware implementation
Author
Nawaz, Zubair ; Bertels, Koen ; Sümbül, H. Ekin
Author_Institution
Comput. Eng. Lab., Delft Univ. of Technol., Delft, Netherlands
fYear
2010
fDate
19-23 April 2010
Firstpage
1
Lastpage
4
Abstract
The Smith-Waterman (SW) algorithm is one of the widely used algorithms for sequence alignment in computational biology. With the growing size of the sequence database, there is always a need for even faster implementation of SW. In this paper, we have implemented two Recursive Variable Expansion (RVE) based techniques, which are proved to give better speedup than any best dataflow approach at the cost of extra area. Compared to dataflow approach, our HW implementation is 2.29 times faster at the expense of 2.82 times more area.
Keywords
algorithm theory; parallel algorithms; recursive functions; systolic arrays; Smith-Waterman algorithm; computational biology; dataflow approach; linear systolic array; recursive variable expansion; Acceleration; Biology computing; Computational biology; Costs; Databases; Field programmable gate arrays; Hardware; Helium; Sequences; Systolic arrays; RVE; computational biology; hardware acceleration; sequence alignment;
fLanguage
English
Publisher
ieee
Conference_Titel
Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW), 2010 IEEE International Symposium on
Conference_Location
Atlanta, GA
Print_ISBN
978-1-4244-6533-0
Type
conf
DOI
10.1109/IPDPSW.2010.5470748
Filename
5470748
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