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
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/103947
Acceder
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oai_identifier_str oai:sedici.unlp.edu.ar:10915/103947
network_acronym_str SEDICI
repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling 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:UNLP2025-10-22T17:03:27Zoai: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:13292025-10-22 17:03:27.258SEDICI (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
format bookPart
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/103947
url http://sedici.unlp.edu.ar/handle/10915/103947
dc.language.none.fl_str_mv spa
language spa
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/isbn/978-3-319-41279-5
info:eu-repo/semantics/altIdentifier/doi/10.1007/978-3-319-41279-5_6
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
197-223
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
instacron:UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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score 12.982451

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