SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences

Background: The Smith-Waterman (SW) algorithm is the best choice for searching similar regions between two DNA or protein sequences. However, it may become impracticable in some contexts due to its high computational demands. Consequently, the computer science community has focused on the use of mod...

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Detalles Bibliográficos
Autores principales: Rucci, Enzo, Garcia, Carlos, Botella, Guillermo, De Giusti, Armando Eduardo, Naiouf, Marcelo, Prieto-Matias, Manuel
Formato: Articulo
Lenguaje:Inglés
Publicado: 2018
Materias:
Ciencias Informáticas
Biología
DNA
Smith-Waterman
OpenCL
High-performance computing
FPGA
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/107848
http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6245597&blobtype=pdf
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-107848
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Informáticas
Biología
DNA
Smith-Waterman
OpenCL
High-performance computing
FPGA
spellingShingle Ciencias Informáticas
Biología
DNA
Smith-Waterman
OpenCL
High-performance computing
FPGA
Rucci, Enzo
Garcia, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
topic_facet Ciencias Informáticas
Biología
DNA
Smith-Waterman
OpenCL
High-performance computing
FPGA
description Background: The Smith-Waterman (SW) algorithm is the best choice for searching similar regions between two DNA or protein sequences. However, it may become impracticable in some contexts due to its high computational demands. Consequently, the computer science community has focused on the use of modern parallel architectures such as Graphics Processing Units (GPUs), Xeon Phi accelerators and Field Programmable Gate Arrays (FGPAs) to speed up large-scale workloads. Results: This paper presents and evaluates SWIFOLD: a Smith-Waterman parallel Implementation on FPGA with OpenCL for Long DNA sequences. First, we evaluate its performance and resource usage for different kernel configurations. Next, we carry out a performance comparison between our tool and other state-of-the-art implementations considering three different datasets. SWIFOLD offers the best average performance for small and medium test sets, achieving a performance that is independent of input size and sequence similarity. In addition, SWIFOLD provides competitive performance rates in comparison with GPU-based implementations on the latest GPU generation for the large dataset. Conclusions: The results suggest that SWIFOLD can be a serious contender for accelerating the SW alignment of DNA sequences of unrestricted size in an affordable way reaching on average 125 GCUPS and almost a peak of 270 GCUPS.
format Articulo
Articulo
author Rucci, Enzo
Garcia, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author_facet Rucci, Enzo
Garcia, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author_sort Rucci, Enzo
title SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
title_short SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
title_full SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
title_fullStr SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
title_full_unstemmed SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
title_sort swifold: smith-waterman implementation on fpga with opencl for long dna sequences
publishDate 2018
url http://sedici.unlp.edu.ar/handle/10915/107848
http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6245597&blobtype=pdf
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