Title :
Optimizing Reconfigurable Hardware for Genomic Sequences Comparison
Author :
Marfil, Juan Jose ; Mozos, Daniel
Author_Institution :
Comput. Archit. Dept., Univ. Complutense de Madrid, Madrid
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;
Conference_Titel :
Programmable Logic, 2008 4th Southern Conference on
Conference_Location :
San Carlos de Bariloche
Print_ISBN :
978-1-4244-1992-0
DOI :
10.1109/SPL.2008.4547763