DocumentCode
2767543
Title
Parallelizing HMMER for Hardware Acceleration on FPGAs
Author
Derrien, Steven ; Quinton, Patrice
Author_Institution
Univ. de Rennes, Rennes
fYear
2007
fDate
9-11 July 2007
Firstpage
10
Lastpage
17
Abstract
Profile based Hidden Markov Model is a widely used tool in bioinformatics. While being very valuable to biologists, it is extremely compute intensive and suffers from prohibitive execution time. We propose an original parallelization scheme of the hmmsearch tool for FPGA technology. We show how to derive a flexible and generic hardware architecture which accelerates the hmmsearch main kernel by two orders of magnitude without modifying its original algorithm.
Keywords
field programmable gate arrays; hidden Markov models; parallel architectures; FPGA parallelization; hardware acceleration; hardware architecture; hidden Markov model; hmmsearch kernel acceleration; hmmsearch tool; Acceleration; Biology computing; Clustering algorithms; Computer architecture; Field programmable gate arrays; Hardware; Hidden Markov models; Kernel; Proteins; Software algorithms;
fLanguage
English
Publisher
ieee
Conference_Titel
Application-specific Systems, Architectures and Processors, 2007. ASAP. IEEE International Conf. on
Conference_Location
Montreal, Que.
ISSN
2160-0511
Print_ISBN
978-1-4244-1026-2
Electronic_ISBN
2160-0511
Type
conf
DOI
10.1109/ASAP.2007.4429951
Filename
4429951
Link To Document