Smith-Waterman Protein Search with OpenCL on an FPGA

The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPU...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Rucci, Enzo, De Giusti, Armando Eduardo, Naiouf, Marcelo, García Sanchez, Carlos, Botella, Juan Guillermo, Prieto-Matias, Manuel
Formato: Objeto de conferencia
Lenguaje:Inglés
Publicado: 2015
Materias:
Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/82865
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
Descripción
Sumario:The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPUs and FPGAs are able to mitigate the computational problems and achieve impressive speedups. In this paper we explore SW acceleration on an FPGA with OpenCL. We efficiently exploit data and thread-level parallelism on an Altera Stratix V FPGA, obtaining up to 39 GCUPS with less than 25 watt of power consumption.

Ejemplares similares