Title :
Parallelizing HMMER for Hardware Acceleration on FPGAs
Author :
Derrien, Steven ; Quinton, Patrice
Author_Institution :
Univ. de Rennes, Rennes
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;
Conference_Titel :
Application-specific Systems, Architectures and Processors, 2007. ASAP. IEEE International Conf. on
Conference_Location :
Montreal, Que.
Print_ISBN :
978-1-4244-1026-2
Electronic_ISBN :
2160-0511
DOI :
10.1109/ASAP.2007.4429951
