OSWALD : openCL Smith–Waterman on Altera’s FPGA for large protein databases

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Detalles Bibliográficos
Autor Principal: Rucci, Enzo
Otros autores o Colaboradores: García, Pablo S., Botella, Guillermo, De Giusti, Armando Eduardo, Naiouf, Ricardo Marcelo, Prieto-Matias, Manuel
Formato: Capítulo de libro
Lengua:inglés
Temas:
ALGORITMOS
bioinformática
Acceso en línea:https://doi.org/10.1177/1094342016654215
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Resumen: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.
Notas:Formato de archivo PDF. -- Este documento es producción intelectual de la Facultad de Informática - UNLP (Colección BIPA/Biblioteca)
Descripción Física:1 archivo (1,1 MB)
DOI:10.1177/1094342016654215

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520 |a 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. 
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700 1 |a Prieto-Matias, Manuel 
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