Improvements in the sensibility of MSA-GA tool using COFFEE objective function
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo de conferência |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://iopscience.iop.org/article/10.1088/1742-6596/574/1/012104/meta http://hdl.handle.net/11449/128820 |
Resumo: | The sequence alignment is one of the most important tasks in Bioinformatics, playing an important role in the sequences analysis. There are many strategies to perform sequence alignment, since those use deterministic algorithms, as dynamic programming, until those ones, which use heuristic algorithms, as Progressive, Ant Colony (ACO), Genetic Algorithms (GA), Simulated Annealing (SA), among others. In this work, we have implemented the objective function COFFEE in the MSA-GA tool, in substitution of Weighted Sum-of-Pairs (WSP), to improve the final results. In the tests, we were able to verify the approach using COFFEE function achieved better results in 81% of the lower similarity alignments when compared with WSP approach. Moreover, even in the tests with more similar sets, the approach using COFFEE was better in 43% of the times. |
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Repositório Institucional da UNESP |
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Improvements in the sensibility of MSA-GA tool using COFFEE objective functionThe sequence alignment is one of the most important tasks in Bioinformatics, playing an important role in the sequences analysis. There are many strategies to perform sequence alignment, since those use deterministic algorithms, as dynamic programming, until those ones, which use heuristic algorithms, as Progressive, Ant Colony (ACO), Genetic Algorithms (GA), Simulated Annealing (SA), among others. In this work, we have implemented the objective function COFFEE in the MSA-GA tool, in substitution of Weighted Sum-of-Pairs (WSP), to improve the final results. In the tests, we were able to verify the approach using COFFEE function achieved better results in 81% of the lower similarity alignments when compared with WSP approach. Moreover, even in the tests with more similar sets, the approach using COFFEE was better in 43% of the times.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de Santa Catarina, Departamento de Engenharia de Controle e AutomaçãoUniversidade Estadual Paulista, Departamento de Ciência da Computação e Estatística, Instituto de Biociências, Letras e Ciências Exatas de São José do Rio PretoFAPESP: 2013/08289-0Iop Publishing LtdUniversidade Estadual Paulista (Unesp)Universidade Federal de Santa Catarina (UFSC)Amorim, Anderson Rici [UNESP]Zafalon, Geraldo Francisco Donegá [UNESP]Neves, Leandro Alves [UNESP]Pinto, Alex Sandro RoschildtValêncio, Carlos Roberto [UNESP]Machado, José Márcio [UNESP]2015-10-21T13:14:01Z2015-10-21T13:14:01Z2015-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObject1-4application/pdfhttp://iopscience.iop.org/article/10.1088/1742-6596/574/1/012104/meta3rd International Conference On Mathematical Modeling In Physical Sciences (IC-MSQUARE 2014). Bristol: Iop Publishing Ltd, v. 574, p. 1-4, 2015.1742-6588http://hdl.handle.net/11449/12882010.1088/1742-6596/574/1/012104WOS:000352595600104WOS000352595600104.pdf213905381487931246448122538758320000-0002-9325-3159Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPeng3rd International Conference On Mathematical Modeling In Physical Sciences (IC-MSQUARE 2014)0,241info:eu-repo/semantics/openAccess2023-10-04T06:08:35Zoai:repositorio.unesp.br:11449/128820Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:01:26.058273Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function |
title |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function |
spellingShingle |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function Amorim, Anderson Rici [UNESP] |
title_short |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function |
title_full |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function |
title_fullStr |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function |
title_full_unstemmed |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function |
title_sort |
Improvements in the sensibility of MSA-GA tool using COFFEE objective function |
author |
Amorim, Anderson Rici [UNESP] |
author_facet |
Amorim, Anderson Rici [UNESP] Zafalon, Geraldo Francisco Donegá [UNESP] Neves, Leandro Alves [UNESP] Pinto, Alex Sandro Roschildt Valêncio, Carlos Roberto [UNESP] Machado, José Márcio [UNESP] |
author_role |
author |
author2 |
Zafalon, Geraldo Francisco Donegá [UNESP] Neves, Leandro Alves [UNESP] Pinto, Alex Sandro Roschildt Valêncio, Carlos Roberto [UNESP] Machado, José Márcio [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade Federal de Santa Catarina (UFSC) |
dc.contributor.author.fl_str_mv |
Amorim, Anderson Rici [UNESP] Zafalon, Geraldo Francisco Donegá [UNESP] Neves, Leandro Alves [UNESP] Pinto, Alex Sandro Roschildt Valêncio, Carlos Roberto [UNESP] Machado, José Márcio [UNESP] |
description |
The sequence alignment is one of the most important tasks in Bioinformatics, playing an important role in the sequences analysis. There are many strategies to perform sequence alignment, since those use deterministic algorithms, as dynamic programming, until those ones, which use heuristic algorithms, as Progressive, Ant Colony (ACO), Genetic Algorithms (GA), Simulated Annealing (SA), among others. In this work, we have implemented the objective function COFFEE in the MSA-GA tool, in substitution of Weighted Sum-of-Pairs (WSP), to improve the final results. In the tests, we were able to verify the approach using COFFEE function achieved better results in 81% of the lower similarity alignments when compared with WSP approach. Moreover, even in the tests with more similar sets, the approach using COFFEE was better in 43% of the times. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015-10-21T13:14:01Z 2015-10-21T13:14:01Z 2015-01-01 |
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://iopscience.iop.org/article/10.1088/1742-6596/574/1/012104/meta 3rd International Conference On Mathematical Modeling In Physical Sciences (IC-MSQUARE 2014). Bristol: Iop Publishing Ltd, v. 574, p. 1-4, 2015. 1742-6588 http://hdl.handle.net/11449/128820 10.1088/1742-6596/574/1/012104 WOS:000352595600104 WOS000352595600104.pdf 2139053814879312 4644812253875832 0000-0002-9325-3159 |
url |
http://iopscience.iop.org/article/10.1088/1742-6596/574/1/012104/meta http://hdl.handle.net/11449/128820 |
identifier_str_mv |
3rd International Conference On Mathematical Modeling In Physical Sciences (IC-MSQUARE 2014). Bristol: Iop Publishing Ltd, v. 574, p. 1-4, 2015. 1742-6588 10.1088/1742-6596/574/1/012104 WOS:000352595600104 WOS000352595600104.pdf 2139053814879312 4644812253875832 0000-0002-9325-3159 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
3rd International Conference On Mathematical Modeling In Physical Sciences (IC-MSQUARE 2014) 0,241 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
1-4 application/pdf |
dc.publisher.none.fl_str_mv |
Iop Publishing Ltd |
publisher.none.fl_str_mv |
Iop Publishing Ltd |
dc.source.none.fl_str_mv |
Web of Science 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 |
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1808128305068507136 |