Smith-Waterman Protein Search with OpenCL on an FPGA

The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPU...

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Detalles Bibliográficos
Autores principales: Rucci, Enzo, De Giusti, Armando Eduardo, Naiouf, Marcelo, García Sanchez, Carlos, Botella, Juan Guillermo, Prieto-Matias, Manuel
Formato: Objeto de conferencia
Lenguaje:Inglés
Publicado: 2015
Materias:
Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/82865
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-82865
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
spellingShingle Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sanchez, Carlos
Botella, Juan Guillermo
Prieto-Matias, Manuel
Smith-Waterman Protein Search with OpenCL on an FPGA
topic_facet Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
description The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPUs and FPGAs are able to mitigate the computational problems and achieve impressive speedups. In this paper we explore SW acceleration on an FPGA with OpenCL. We efficiently exploit data and thread-level parallelism on an Altera Stratix V FPGA, obtaining up to 39 GCUPS with less than 25 watt of power consumption.
format Objeto de conferencia
Objeto de conferencia
author Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sanchez, Carlos
Botella, Juan Guillermo
Prieto-Matias, Manuel
author_facet Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sanchez, Carlos
Botella, Juan Guillermo
Prieto-Matias, Manuel
author_sort Rucci, Enzo
title Smith-Waterman Protein Search with OpenCL on an FPGA
title_short Smith-Waterman Protein Search with OpenCL on an FPGA
title_full Smith-Waterman Protein Search with OpenCL on an FPGA
title_fullStr Smith-Waterman Protein Search with OpenCL on an FPGA
title_full_unstemmed Smith-Waterman Protein Search with OpenCL on an FPGA
title_sort smith-waterman protein search with opencl on an fpga
publishDate 2015
url http://sedici.unlp.edu.ar/handle/10915/82865
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