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
Descripción
Sumario: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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