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

Autores
Rucci, Enzo; García Sanchez, Carlos; Botella, Guillermo Juan; de Giusti, Armando Eduardo; Naiouf, Ricardo Marcelo; Prieto Matías, Manuel
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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 (FPGAs) 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.
Fil: Rucci, Enzo. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
Fil: García Sanchez, Carlos. Universidad Complutense de Madrid; España
Fil: Botella, Guillermo Juan. Universidad Complutense de Madrid; España
Fil: de Giusti, Armando Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; Argentina
Fil: Naiouf, Ricardo Marcelo. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; Argentina
Fil: Prieto Matías, Manuel. Universidad Complutense de Madrid; España
Materia
DNA
Smith-Waterman
OpenCL
HPC
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/100986
Acceder
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling SWIFOLD: Smith-Waterman Implementation on FPGA with OpenCL for long DNA sequencesRucci, EnzoGarcía Sanchez, CarlosBotella, Guillermo Juande Giusti, Armando EduardoNaiouf, Ricardo MarceloPrieto Matías, ManuelDNASmith-WatermanOpenCLHPChttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Background: 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 (FPGAs) 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.Fil: Rucci, Enzo. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: García Sanchez, Carlos. Universidad Complutense de Madrid; EspañaFil: Botella, Guillermo Juan. Universidad Complutense de Madrid; EspañaFil: de Giusti, Armando Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; ArgentinaFil: Naiouf, Ricardo Marcelo. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; ArgentinaFil: Prieto Matías, Manuel. Universidad Complutense de Madrid; EspañaBioMed Central2018-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/zipapplication/pdfhttp://hdl.handle.net/11336/100986Rucci, Enzo; García Sanchez, Carlos; Botella, Guillermo Juan; de Giusti, Armando Eduardo; Naiouf, Ricardo Marcelo; et al.; SWIFOLD: Smith-Waterman Implementation on FPGA with OpenCL for long DNA sequences; BioMed Central; Bmc Systems Biology; 12; 96; 2-2018; 43-531752-0509CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1186%2Fs12918-018-0614-6info:eu-repo/semantics/altIdentifier/doi/10.1186/s12918-018-0614-6info:eu-repo/semantics/altIdentifier/url/https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-018-0614-6info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:45:20Zoai:ri.conicet.gov.ar:11336/100986instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:45:20.655CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv SWIFOLD: Smith-Waterman Implementation on FPGA with OpenCL for long DNA sequences
title SWIFOLD: Smith-Waterman Implementation on FPGA with OpenCL for long DNA sequences
spellingShingle SWIFOLD: Smith-Waterman Implementation on FPGA with OpenCL for long DNA sequences
Rucci, Enzo
DNA
Smith-Waterman
OpenCL
HPC
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
dc.creator.none.fl_str_mv Rucci, Enzo
García Sanchez, Carlos
Botella, Guillermo Juan
de Giusti, Armando Eduardo
Naiouf, Ricardo Marcelo
Prieto Matías, Manuel
author Rucci, Enzo
author_facet Rucci, Enzo
García Sanchez, Carlos
Botella, Guillermo Juan
de Giusti, Armando Eduardo
Naiouf, Ricardo Marcelo
Prieto Matías, Manuel
author_role author
author2 García Sanchez, Carlos
Botella, Guillermo Juan
de Giusti, Armando Eduardo
Naiouf, Ricardo Marcelo
Prieto Matías, Manuel
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv DNA
Smith-Waterman
OpenCL
HPC
topic DNA
Smith-Waterman
OpenCL
HPC
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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 (FPGAs) 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.
Fil: Rucci, Enzo. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
Fil: García Sanchez, Carlos. Universidad Complutense de Madrid; España
Fil: Botella, Guillermo Juan. Universidad Complutense de Madrid; España
Fil: de Giusti, Armando Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; Argentina
Fil: Naiouf, Ricardo Marcelo. Universidad Nacional de la Plata. Facultad de Informatica. Instituto de Investigación En Informatica Lidi; Argentina
Fil: Prieto Matías, Manuel. Universidad Complutense de Madrid; España
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 (FPGAs) 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.
publishDate 2018
dc.date.none.fl_str_mv 2018-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/100986
Rucci, Enzo; García Sanchez, Carlos; Botella, Guillermo Juan; de Giusti, Armando Eduardo; Naiouf, Ricardo Marcelo; et al.; SWIFOLD: Smith-Waterman Implementation on FPGA with OpenCL for long DNA sequences; BioMed Central; Bmc Systems Biology; 12; 96; 2-2018; 43-53
1752-0509
CONICET Digital
CONICET
url http://hdl.handle.net/11336/100986
identifier_str_mv Rucci, Enzo; García Sanchez, Carlos; Botella, Guillermo Juan; de Giusti, Armando Eduardo; Naiouf, Ricardo Marcelo; et al.; SWIFOLD: Smith-Waterman Implementation on FPGA with OpenCL for long DNA sequences; BioMed Central; Bmc Systems Biology; 12; 96; 2-2018; 43-53
1752-0509
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1186%2Fs12918-018-0614-6
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12918-018-0614-6
info:eu-repo/semantics/altIdentifier/url/https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-018-0614-6
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/zip
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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