State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms
- Autores
- Rucci, Enzo; García Sánchez, Carlos; Botella, Guillermo; De Giusti, Armando Eduardo; Naiouf, Marcelo; Prieto-Matías, Manuel; Wong, Ka-Chun
- Año de publicación
- 2016
- Idioma
- español castellano
- Tipo de recurso
- parte de libro
- Estado
- versión publicada
- Descripción
- Searching biological sequence database is a common and repeated task in bioinformatics and molecular biology. The Smith–Waterman algorithm is the most accurate method for this kind of search. Unfortunately, this algorithm is computationally demanding and the situation gets worse due to the exponential growth of biological data in the last years. For that reason, the scientific community has made great efforts to accelerate Smith–Waterman biological database searches in a wide variety of hardware platforms. We give a survey of the state-of-the-art in Smith–Waterman protein database search, focusing on four hardware architectures: central processing units, graphics processing units, field programmable gate arrays and Xeon Phi coprocessors. After briefly describing each hardware platform, we analyse temporal evolution, contributions, limitations and experimental work and the results of each implementation. Additionally, as energy efficiency is becoming more important every day, we also survey performance/power consumption works. Finally, we give our view on the future of Smith–Waterman protein searches considering next generations of hardware architectures and its upcoming technologies.
Instituto de Investigación en Informática
Universidad Complutense de Madrid - Materia
-
Ciencias Informáticas
Molecular biology
Bioinformatics
Algorithms - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- http://creativecommons.org/licenses/by-nc-sa/4.0/
- Repositorio
- Institución
- Universidad Nacional de La Plata
- OAI Identificador
- oai:sedici.unlp.edu.ar:10915/103947
Ver los metadatos del registro completo
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State-of-the-art in Smith-Waterman Protein Database Search on HPC PlatformsRucci, EnzoGarcía Sánchez, CarlosBotella, GuillermoDe Giusti, Armando EduardoNaiouf, MarceloPrieto-Matías, ManuelWong, Ka-ChunCiencias InformáticasMolecular biologyBioinformaticsAlgorithmsSearching biological sequence database is a common and repeated task in bioinformatics and molecular biology. The Smith–Waterman algorithm is the most accurate method for this kind of search. Unfortunately, this algorithm is computationally demanding and the situation gets worse due to the exponential growth of biological data in the last years. For that reason, the scientific community has made great efforts to accelerate Smith–Waterman biological database searches in a wide variety of hardware platforms. We give a survey of the state-of-the-art in Smith–Waterman protein database search, focusing on four hardware architectures: central processing units, graphics processing units, field programmable gate arrays and Xeon Phi coprocessors. After briefly describing each hardware platform, we analyse temporal evolution, contributions, limitations and experimental work and the results of each implementation. Additionally, as energy efficiency is becoming more important every day, we also survey performance/power consumption works. Finally, we give our view on the future of Smith–Waterman protein searches considering next generations of hardware architectures and its upcoming technologies.Instituto de Investigación en InformáticaUniversidad Complutense de MadridSpringer2016-10-25info:eu-repo/semantics/bookPartinfo:eu-repo/semantics/publishedVersionCapitulo de librohttp://purl.org/coar/resource_type/c_3248info:ar-repo/semantics/parteDeLibroapplication/pdf197-223http://sedici.unlp.edu.ar/handle/10915/103947spainfo:eu-repo/semantics/altIdentifier/isbn/978-3-319-41279-5info:eu-repo/semantics/altIdentifier/doi/10.1007/978-3-319-41279-5_6info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:22:33Zoai:sedici.unlp.edu.ar:10915/103947Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:22:34.286SEDICI (UNLP) - Universidad Nacional de La Platafalse |
dc.title.none.fl_str_mv |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms |
title |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms |
spellingShingle |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms Rucci, Enzo Ciencias Informáticas Molecular biology Bioinformatics Algorithms |
title_short |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms |
title_full |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms |
title_fullStr |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms |
title_full_unstemmed |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms |
title_sort |
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms |
dc.creator.none.fl_str_mv |
Rucci, Enzo García Sánchez, Carlos Botella, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matías, Manuel Wong, Ka-Chun |
author |
Rucci, Enzo |
author_facet |
Rucci, Enzo García Sánchez, Carlos Botella, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matías, Manuel Wong, Ka-Chun |
author_role |
author |
author2 |
García Sánchez, Carlos Botella, Guillermo De Giusti, Armando Eduardo Naiouf, Marcelo Prieto-Matías, Manuel Wong, Ka-Chun |
author2_role |
author author author author author author |
dc.subject.none.fl_str_mv |
Ciencias Informáticas Molecular biology Bioinformatics Algorithms |
topic |
Ciencias Informáticas Molecular biology Bioinformatics Algorithms |
dc.description.none.fl_txt_mv |
Searching biological sequence database is a common and repeated task in bioinformatics and molecular biology. The Smith–Waterman algorithm is the most accurate method for this kind of search. Unfortunately, this algorithm is computationally demanding and the situation gets worse due to the exponential growth of biological data in the last years. For that reason, the scientific community has made great efforts to accelerate Smith–Waterman biological database searches in a wide variety of hardware platforms. We give a survey of the state-of-the-art in Smith–Waterman protein database search, focusing on four hardware architectures: central processing units, graphics processing units, field programmable gate arrays and Xeon Phi coprocessors. After briefly describing each hardware platform, we analyse temporal evolution, contributions, limitations and experimental work and the results of each implementation. Additionally, as energy efficiency is becoming more important every day, we also survey performance/power consumption works. Finally, we give our view on the future of Smith–Waterman protein searches considering next generations of hardware architectures and its upcoming technologies. Instituto de Investigación en Informática Universidad Complutense de Madrid |
description |
Searching biological sequence database is a common and repeated task in bioinformatics and molecular biology. The Smith–Waterman algorithm is the most accurate method for this kind of search. Unfortunately, this algorithm is computationally demanding and the situation gets worse due to the exponential growth of biological data in the last years. For that reason, the scientific community has made great efforts to accelerate Smith–Waterman biological database searches in a wide variety of hardware platforms. We give a survey of the state-of-the-art in Smith–Waterman protein database search, focusing on four hardware architectures: central processing units, graphics processing units, field programmable gate arrays and Xeon Phi coprocessors. After briefly describing each hardware platform, we analyse temporal evolution, contributions, limitations and experimental work and the results of each implementation. Additionally, as energy efficiency is becoming more important every day, we also survey performance/power consumption works. Finally, we give our view on the future of Smith–Waterman protein searches considering next generations of hardware architectures and its upcoming technologies. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-10-25 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/bookPart info:eu-repo/semantics/publishedVersion Capitulo de libro http://purl.org/coar/resource_type/c_3248 info:ar-repo/semantics/parteDeLibro |
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http://sedici.unlp.edu.ar/handle/10915/103947 |
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http://sedici.unlp.edu.ar/handle/10915/103947 |
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language |
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openAccess |
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http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) |
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application/pdf 197-223 |
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Springer |
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Springer |
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