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
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;
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
DOI :
10.1109/IPDPSW.2010.5470748
