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
- Institución
- Universidad Nacional de La Plata
- OAI Identificador
- oai:sedici.unlp.edu.ar:10915/82889
Ver los metadatos del registro completo
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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 |
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http://sedici.unlp.edu.ar/handle/10915/82889 |
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eng |
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eng |
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info:eu-repo/semantics/altIdentifier/issn/1741-2846 info:eu-repo/semantics/altIdentifier/doi/10.1177/1094342016654215 |
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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) |
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