OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases

The well-known Smith–Waterman algorithm is a high-sensitivity method for local sequence alignment. Unfortunately, the Smith–Waterman algorithm has quadratic time complexity, which makes it computationally demanding for large protein databases. In this paper, we present OSWALD, a portable, fully func...

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Detalles Bibliográficos
Autores principales:	Rucci, Enzo, García Sénchez, Carlos, Botella Juan, Guillermo, De Giusti, Armando Eduardo, Naiouf, Marcelo, Prieto-Matias, Manuel
Formato:	Articulo
Lenguaje:	Inglés
Publicado:	2016
Materias:	Ciencias Informáticas Bioinformatics Smith-Waterman FPGA Altera OpenCL
Acceso en línea:	http://sedici.unlp.edu.ar/handle/10915/82889
Aporte de:	SEDICI (UNLP) de Universidad Nacional de La Plata

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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 García Sénchez, Carlos Botella Juan, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matias, Manuel OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
topic_facet	Ciencias Informáticas Bioinformatics Smith-Waterman FPGA Altera OpenCL
description	The well-known Smith–Waterman algorithm is a high-sensitivity method for local sequence alignment. Unfortunately, the Smith–Waterman algorithm has quadratic time complexity, which makes it computationally demanding for large protein databases. In this paper, we present OSWALD, a portable, fully functional and general implementation to accelerate Smith–Waterman database searches in heterogeneous platforms based on Altera’s FPGA. OSWALD exploits OpenMP multithreading and SIMD computing through SSE and AVX2 extensions on the host while taking advantage of pipeline and vectorial parallelism by way of OpenCL on the FPGAs. Performance evaluations on two different heterogeneous architectures with real amino acid datasets show that OSWALD is competitive in comparison with other top-performing Smith–Waterman implementations, attaining up to 442 GCUPS peak with the best GCUPS/watts ratio.
format	Articulo Articulo
author	Rucci, Enzo García Sénchez, Carlos Botella Juan, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matias, Manuel
author_facet	Rucci, Enzo García Sénchez, Carlos Botella Juan, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matias, Manuel
author_sort	Rucci, Enzo
title	OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
title_short	OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
title_full	OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
title_fullStr	OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
title_full_unstemmed	OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
title_sort	oswald: opencl smith–waterman on altera’s fpga for large protein databases
publishDate	2016
url	http://sedici.unlp.edu.ar/handle/10915/82889
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OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases

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