State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms

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 exponenti...

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Detalles Bibliográficos
Autores principales: Rucci, Enzo, García Sánchez, Carlos, Botella, Guillermo, De Giusti, Armando Eduardo, Naiouf, Marcelo, Prieto-Matías, Manuel, Wong, Ka-Chun
Formato: Libro Capitulo de libro
Lenguaje:Español
Publicado: Springer 2016
Materias:
Ciencias Informáticas
Molecular biology
Bioinformatics
Algorithms
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/103947
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-103947
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Español
topic Ciencias Informáticas
Molecular biology
Bioinformatics
Algorithms
spellingShingle Ciencias Informáticas
Molecular biology
Bioinformatics
Algorithms
Rucci, Enzo
García Sánchez, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matías, Manuel
Wong, Ka-Chun
State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms
topic_facet Ciencias Informáticas
Molecular biology
Bioinformatics
Algorithms
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.
format Libro
Capitulo de libro
author Rucci, Enzo
García Sánchez, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matías, Manuel
Wong, Ka-Chun
author_facet Rucci, Enzo
García Sánchez, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matías, Manuel
Wong, Ka-Chun
author_sort Rucci, Enzo
title State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms
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
publisher Springer
publishDate 2016
url http://sedici.unlp.edu.ar/handle/10915/103947
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