DocumentCode :
1921553
Title :
Optimizing Reconfigurable Hardware for Genomic Sequences Comparison
Author :
Marfil, Juan Jose ; Mozos, Daniel
Author_Institution :
Comput. Archit. Dept., Univ. Complutense de Madrid, Madrid
fYear :
2008
fDate :
26-28 March 2008
Firstpage :
225
Lastpage :
228
Abstract :
Last advances in the bioinformatics field have lead to improve models and computational resources to satisfy the high computational cost needed to search and identify DNA sequences. This paper provides a FPGA-based systolic array implementation of the Smith-Waterman algorithm, which improves previous proposals, reducing the amount of hardware and the computing power needed. Besides, optimizations in memory access using prefetching and different sizes of the systolic array let us to increase the system´s performance up to 60%.
Keywords :
biology computing; field programmable gate arrays; genetic engineering; reconfigurable architectures; systolic arrays; DNA sequences; FPGA-based systolic array; bioinformatics field; genomic sequences comparison; reconfigurable hardware; Bioinformatics; Computational efficiency; Computational modeling; DNA computing; Genomics; Hardware; Prefetching; Proposals; Sequences; Systolic arrays;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Programmable Logic, 2008 4th Southern Conference on
Conference_Location :
San Carlos de Bariloche
Print_ISBN :
978-1-4244-1992-0
Type :
conf
DOI :
10.1109/SPL.2008.4547763
Filename :
4547763
Link To Document :
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