A parallel approach of COFFEE objective function to multiple sequence alignment

Detalhes bibliográficos
Autor(a) principal: Zafalon, G. F.D. [UNESP]
Data de Publicação: 2015
Outros Autores: Visotaky, J. M.V. [UNESP], Amorim, A. R. [UNESP], Valêncio, C. R. [UNESP], Neves, L. A. [UNESP], De Souza, R. C.G. [UNESP], Machado, J. M. [UNESP]
Tipo de documento: Artigo de conferência
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1088/1742-6596/633/1/012084
http://hdl.handle.net/11449/173403
Resumo: The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.
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spelling A parallel approach of COFFEE objective function to multiple sequence alignmentThe computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.Department of Computer Science and Statistics (DCCE) São Paulo State University (UNESP)Department of Computer Science and Statistics (DCCE) São Paulo State University (UNESP)Universidade Estadual Paulista (Unesp)Zafalon, G. F.D. [UNESP]Visotaky, J. M.V. [UNESP]Amorim, A. R. [UNESP]Valêncio, C. R. [UNESP]Neves, L. A. [UNESP]De Souza, R. C.G. [UNESP]Machado, J. M. [UNESP]2018-12-11T17:05:02Z2018-12-11T17:05:02Z2015-09-21info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectapplication/pdfhttp://dx.doi.org/10.1088/1742-6596/633/1/012084Journal of Physics: Conference Series, v. 633, n. 1, 2015.1742-65961742-6588http://hdl.handle.net/11449/17340310.1088/1742-6596/633/1/0120842-s2.0-849835436292-s2.0-84983543629.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Physics: Conference Series0,2410,241info:eu-repo/semantics/openAccess2023-11-11T06:11:04Zoai:repositorio.unesp.br:11449/173403Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:22:36.018790Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv A parallel approach of COFFEE objective function to multiple sequence alignment
title A parallel approach of COFFEE objective function to multiple sequence alignment
spellingShingle A parallel approach of COFFEE objective function to multiple sequence alignment
Zafalon, G. F.D. [UNESP]
title_short A parallel approach of COFFEE objective function to multiple sequence alignment
title_full A parallel approach of COFFEE objective function to multiple sequence alignment
title_fullStr A parallel approach of COFFEE objective function to multiple sequence alignment
title_full_unstemmed A parallel approach of COFFEE objective function to multiple sequence alignment
title_sort A parallel approach of COFFEE objective function to multiple sequence alignment
author Zafalon, G. F.D. [UNESP]
author_facet Zafalon, G. F.D. [UNESP]
Visotaky, J. M.V. [UNESP]
Amorim, A. R. [UNESP]
Valêncio, C. R. [UNESP]
Neves, L. A. [UNESP]
De Souza, R. C.G. [UNESP]
Machado, J. M. [UNESP]
author_role author
author2 Visotaky, J. M.V. [UNESP]
Amorim, A. R. [UNESP]
Valêncio, C. R. [UNESP]
Neves, L. A. [UNESP]
De Souza, R. C.G. [UNESP]
Machado, J. M. [UNESP]
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv Zafalon, G. F.D. [UNESP]
Visotaky, J. M.V. [UNESP]
Amorim, A. R. [UNESP]
Valêncio, C. R. [UNESP]
Neves, L. A. [UNESP]
De Souza, R. C.G. [UNESP]
Machado, J. M. [UNESP]
description The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.
publishDate 2015
dc.date.none.fl_str_mv 2015-09-21
2018-12-11T17:05:02Z
2018-12-11T17:05:02Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/conferenceObject
format conferenceObject
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1088/1742-6596/633/1/012084
Journal of Physics: Conference Series, v. 633, n. 1, 2015.
1742-6596
1742-6588
http://hdl.handle.net/11449/173403
10.1088/1742-6596/633/1/012084
2-s2.0-84983543629
2-s2.0-84983543629.pdf
url http://dx.doi.org/10.1088/1742-6596/633/1/012084
http://hdl.handle.net/11449/173403
identifier_str_mv Journal of Physics: Conference Series, v. 633, n. 1, 2015.
1742-6596
1742-6588
10.1088/1742-6596/633/1/012084
2-s2.0-84983543629
2-s2.0-84983543629.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Journal of Physics: Conference Series
0,241
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dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
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repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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