Title :
Hardware implementation of the Smith-Waterman Algorithm using Recursive Variable Expansion
Author :
Hasan, Laiq ; Al-Ars, Zaid ; Nawaz, Zubair ; Bertels, Koen
Author_Institution :
Comput. Eng. Lab., Delft Univ. of Technol., Delft
Abstract :
In this paper we adapted a novel approach for accelerating the Smith-Waterman (S-W) algorithm using Recursive Variable Expansion (RVE), which exposes extra parallelism in the algorithm, as compared to any other technique. The results demonstrate that applying the recursive variable expansion technique speeds up the performance by a factor of 1.36 to 1.41, as compared to traditional acceleration approaches at the cost of using 1.25 to 1.28 times more hardware resources.
Keywords :
bioinformatics; field programmable gate arrays; parallel algorithms; FPGA; Smith-Waterman algorithm; bioinformatics; hardware implementation; hardware resources; recursive variable expansion; Acceleration; Concurrent computing; Costs; Equations; Field programmable gate arrays; Hardware; Laboratories; Parallel processing; Sequences; Systolic arrays; FPGA; Recursive Variable Expansion; Sequence Alignment; Smith-Waterman Algorithm; Systolic Array;
Conference_Titel :
Design and Test Workshop, 2008. IDT 2008. 3rd International
Conference_Location :
Monastir
Print_ISBN :
978-1-4244-3479-4
Electronic_ISBN :
978-1-4244-3478-7
DOI :
10.1109/IDT.2008.4802483
