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

Autores
Rucci, Enzo; García Sénchez, Carlos; Botella Juan, Guillermo; De Giusti, Armando Eduardo; Naiouf, Marcelo; Prieto-Matias, Manuel
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
First published June 30, 2016. Article available in: Vol. 32, Issue 3, 2018.
Facultad de Informática
Materia
Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-nd/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/82889

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network_name_str SEDICI (UNLP)
spelling OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein DatabasesRucci, EnzoGarcía Sénchez, CarlosBotella Juan, GuillermoDe Giusti, Armando EduardoNaiouf, MarceloPrieto-Matias, ManuelCiencias InformáticasBioinformaticsSmith-WatermanFPGAAlteraOpenCLThe 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.First published June 30, 2016. Article available in: Vol. 32, Issue 3, 2018.Facultad de Informática2016-06-30info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://sedici.unlp.edu.ar/handle/10915/82889enginfo:eu-repo/semantics/altIdentifier/issn/1741-2846info:eu-repo/semantics/altIdentifier/doi/10.1177/1094342016654215info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-nd/4.0/Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:15:36Zoai:sedici.unlp.edu.ar:10915/82889Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:15:37.203SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
title OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
spellingShingle OSWALD: OpenCL Smith–Waterman on Altera’s FPGA for Large Protein Databases
Rucci, Enzo
Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
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
dc.creator.none.fl_str_mv Rucci, Enzo
García Sénchez, Carlos
Botella Juan, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author Rucci, Enzo
author_facet Rucci, Enzo
García Sénchez, Carlos
Botella Juan, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author_role author
author2 García Sénchez, Carlos
Botella Juan, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
topic Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
dc.description.none.fl_txt_mv 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.
First published June 30, 2016. Article available in: Vol. 32, Issue 3, 2018.
Facultad de Informática
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.
publishDate 2016
dc.date.none.fl_str_mv 2016-06-30
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
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status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/82889
url http://sedici.unlp.edu.ar/handle/10915/82889
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/1741-2846
info:eu-repo/semantics/altIdentifier/doi/10.1177/1094342016654215
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
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reponame_str SEDICI (UNLP)
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repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
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