Improvements in the score matrix calculation method using parallel score estimating algorithm
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://www.scirp.org/journal/PaperInformation.aspx?PaperID=31755#.VS1BofnF9sw http://hdl.handle.net/11449/122580 |
Resumo: | The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming. |
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Repositório Institucional da UNESP |
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Improvements in the score matrix calculation method using parallel score estimating algorithmAlgorithmsScoring MatrixParallel ProgrammingAlignment QualityThe increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.Universidade Estadual Paulista Júlio de Mesquita Filho, Departamento de Ciência da Computação e Estatística, Instituto de Biociências Letras e Ciências Exatas de São José do Rio Preto, São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, CEP 15054000, SP, BrasilUniversidade Estadual Paulista Júlio de Mesquita Filho, Departamento de Ciência da Computação e Estatística, Instituto de Biociências Letras e Ciências Exatas de São José do Rio Preto, São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, CEP 15054000, SP, BrasilEscola Politécnica University of São Paulo Av. Prof. Luciano Gualberto, São Paulo, Brazil;Universidade Estadual Paulista (Unesp)Zafalon, Geraldo F. D. [UNESP]Marucci, Evandro A. [UNESP]Momente, Julio C. [UNESP]Amazonas, José R. A.Sato, Liria M.Machado, José Marcio [UNESP]2015-04-27T11:55:52Z2015-04-27T11:55:52Z2013info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article47-51application/pdfhttp://www.scirp.org/journal/PaperInformation.aspx?PaperID=31755#.VS1BofnF9swJournal of Biophysical Chemistry, v. 04, n. 02, p. 47-51, 2013.2153-0378http://hdl.handle.net/11449/12258010.4236/jbpc.2013.42006ISSN2153-0378-2013-04-02-47-51.pdf7493638629090475Currículo Lattesreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Biophysical Chemistryinfo:eu-repo/semantics/openAccess2023-11-28T06:18:11Zoai:repositorio.unesp.br:11449/122580Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-11-28T06:18:11Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Improvements in the score matrix calculation method using parallel score estimating algorithm |
title |
Improvements in the score matrix calculation method using parallel score estimating algorithm |
spellingShingle |
Improvements in the score matrix calculation method using parallel score estimating algorithm Zafalon, Geraldo F. D. [UNESP] Algorithms Scoring Matrix Parallel Programming Alignment Quality |
title_short |
Improvements in the score matrix calculation method using parallel score estimating algorithm |
title_full |
Improvements in the score matrix calculation method using parallel score estimating algorithm |
title_fullStr |
Improvements in the score matrix calculation method using parallel score estimating algorithm |
title_full_unstemmed |
Improvements in the score matrix calculation method using parallel score estimating algorithm |
title_sort |
Improvements in the score matrix calculation method using parallel score estimating algorithm |
author |
Zafalon, Geraldo F. D. [UNESP] |
author_facet |
Zafalon, Geraldo F. D. [UNESP] Marucci, Evandro A. [UNESP] Momente, Julio C. [UNESP] Amazonas, José R. A. Sato, Liria M. Machado, José Marcio [UNESP] |
author_role |
author |
author2 |
Marucci, Evandro A. [UNESP] Momente, Julio C. [UNESP] Amazonas, José R. A. Sato, Liria M. Machado, José Marcio [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Zafalon, Geraldo F. D. [UNESP] Marucci, Evandro A. [UNESP] Momente, Julio C. [UNESP] Amazonas, José R. A. Sato, Liria M. Machado, José Marcio [UNESP] |
dc.subject.por.fl_str_mv |
Algorithms Scoring Matrix Parallel Programming Alignment Quality |
topic |
Algorithms Scoring Matrix Parallel Programming Alignment Quality |
description |
The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming. |
publishDate |
2013 |
dc.date.none.fl_str_mv |
2013 2015-04-27T11:55:52Z 2015-04-27T11:55:52Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://www.scirp.org/journal/PaperInformation.aspx?PaperID=31755#.VS1BofnF9sw Journal of Biophysical Chemistry, v. 04, n. 02, p. 47-51, 2013. 2153-0378 http://hdl.handle.net/11449/122580 10.4236/jbpc.2013.42006 ISSN2153-0378-2013-04-02-47-51.pdf 7493638629090475 |
url |
http://www.scirp.org/journal/PaperInformation.aspx?PaperID=31755#.VS1BofnF9sw http://hdl.handle.net/11449/122580 |
identifier_str_mv |
Journal of Biophysical Chemistry, v. 04, n. 02, p. 47-51, 2013. 2153-0378 10.4236/jbpc.2013.42006 ISSN2153-0378-2013-04-02-47-51.pdf 7493638629090475 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Biophysical Chemistry |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
47-51 application/pdf |
dc.source.none.fl_str_mv |
Currículo Lattes reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1797789845575172096 |