TY  - GEN
T1  - OSWALD : openCL Smith–Waterman on Altera’s FPGA for large protein databases
A1  - Rucci, Enzo
A2  - García, Pablo S.
A2  - Botella, Guillermo
A2  - De Giusti, Armando Eduardo
A2  - Naiouf, Ricardo Marcelo
A2  - Prieto-Matias, Manuel
LA  - English
UL  - http://vufind10-pruebas.sigbunlp.bibliotecas.unlp.edu.ar/Record/dif.56853
AB  - 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.
NO  - Formato de archivo PDF. -- Este documento es producción intelectual de la Facultad de Informática - UNLP (Colección BIPA/Biblioteca)
KW  - ALGORITMOS
KW  - bioinformática
ER  -