A Characteristic-Based Framework for Multiple Sequence Aligners

Detalhes bibliográficos
Autor(a) principal: Rubio-Largo, Álvaro
Data de Publicação: 2018
Outros Autores: Vanneschi, Leonardo, Castelli, Mauro, Vega-Rodriguez, Miguel A.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/146530
Resumo: Rubio-Largo, Á., Vanneschi, L., Castelli, M., & Vega-Rodriguez, M. A. (2018). A Characteristic-Based Framework for Multiple Sequence Aligners. IEEE Transactions on Cybernetics, 48(1), 41-51. DOI: 10.1109/TCYB.2016.2621129
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spelling A Characteristic-Based Framework for Multiple Sequence AlignersCharacteristics-basedMultiple sequence alignment (MSA)Particle swarm optimization (PSO)Control and Systems EngineeringSoftwareInformation SystemsHuman-Computer InteractionComputer Science ApplicationsElectrical and Electronic EngineeringSDG 3 - Good Health and Well-beingRubio-Largo, Á., Vanneschi, L., Castelli, M., & Vega-Rodriguez, M. A. (2018). A Characteristic-Based Framework for Multiple Sequence Aligners. IEEE Transactions on Cybernetics, 48(1), 41-51. DOI: 10.1109/TCYB.2016.2621129The multiple sequence alignment is a well-known bioinformatics problem that consists in the alignment of three or more biological sequences (protein or nucleic acid). In the literature, a number of tools have been proposed for dealing with this biological sequence alignment problem, such as progressive methods, consistency-based methods, or iterative methods; among others. These aligners often use a default parameter configuration for all the input sequences to align. However, the default configuration is not always the best choice, the alignment accuracy of the tool may be highly boosted if specific parameter configurations are used, depending on the biological characteristics of the input sequences. In this paper, we propose a characteristic-based framework for multiple sequence aligners. The idea of the framework is, given an input set of unaligned sequences, extract its characteristics and run the aligner with the best parameter configuration found for another set of unaligned sequences with similar characteristics. In order to test the framework, we have used the well-known multiple sequence comparison by log-expectation (MUSCLE) v3.8 aligner with different benchmarks, such as benchmark alignments database v3.0, protein reference alignment benchmark v4.0, and sequence alignment benchmark v1.65. The results shown that the alignment accuracy and conservation of MUSCLE might be greatly improved with the proposed framework, specially in those scenarios with a low percentage of identity. The characteristic-based framework for multiple sequence aligners is freely available for downloading at http://arco.unex.es/arl/fwk-msa/cbf-msa.zipNOVA Information Management School (NOVA IMS)Information Management Research Center (MagIC) - NOVA Information Management SchoolRUNRubio-Largo, ÁlvaroVanneschi, LeonardoCastelli, MauroVega-Rodriguez, Miguel A.2022-12-22T22:09:31Z2018-012018-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article10application/pdfhttp://hdl.handle.net/10362/146530eng2168-2267PURE: 3236493https://doi.org/10.1109/TCYB.2016.2621129info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:27:39Zoai:run.unl.pt:10362/146530Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:52:40.401036Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv A Characteristic-Based Framework for Multiple Sequence Aligners
title A Characteristic-Based Framework for Multiple Sequence Aligners
spellingShingle A Characteristic-Based Framework for Multiple Sequence Aligners
Rubio-Largo, Álvaro
Characteristics-based
Multiple sequence alignment (MSA)
Particle swarm optimization (PSO)
Control and Systems Engineering
Software
Information Systems
Human-Computer Interaction
Computer Science Applications
Electrical and Electronic Engineering
SDG 3 - Good Health and Well-being
title_short A Characteristic-Based Framework for Multiple Sequence Aligners
title_full A Characteristic-Based Framework for Multiple Sequence Aligners
title_fullStr A Characteristic-Based Framework for Multiple Sequence Aligners
title_full_unstemmed A Characteristic-Based Framework for Multiple Sequence Aligners
title_sort A Characteristic-Based Framework for Multiple Sequence Aligners
author Rubio-Largo, Álvaro
author_facet Rubio-Largo, Álvaro
Vanneschi, Leonardo
Castelli, Mauro
Vega-Rodriguez, Miguel A.
author_role author
author2 Vanneschi, Leonardo
Castelli, Mauro
Vega-Rodriguez, Miguel A.
author2_role author
author
author
dc.contributor.none.fl_str_mv NOVA Information Management School (NOVA IMS)
Information Management Research Center (MagIC) - NOVA Information Management School
RUN
dc.contributor.author.fl_str_mv Rubio-Largo, Álvaro
Vanneschi, Leonardo
Castelli, Mauro
Vega-Rodriguez, Miguel A.
dc.subject.por.fl_str_mv Characteristics-based
Multiple sequence alignment (MSA)
Particle swarm optimization (PSO)
Control and Systems Engineering
Software
Information Systems
Human-Computer Interaction
Computer Science Applications
Electrical and Electronic Engineering
SDG 3 - Good Health and Well-being
topic Characteristics-based
Multiple sequence alignment (MSA)
Particle swarm optimization (PSO)
Control and Systems Engineering
Software
Information Systems
Human-Computer Interaction
Computer Science Applications
Electrical and Electronic Engineering
SDG 3 - Good Health and Well-being
description Rubio-Largo, Á., Vanneschi, L., Castelli, M., & Vega-Rodriguez, M. A. (2018). A Characteristic-Based Framework for Multiple Sequence Aligners. IEEE Transactions on Cybernetics, 48(1), 41-51. DOI: 10.1109/TCYB.2016.2621129
publishDate 2018
dc.date.none.fl_str_mv 2018-01
2018-01-01T00:00:00Z
2022-12-22T22:09:31Z
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://hdl.handle.net/10362/146530
url http://hdl.handle.net/10362/146530
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 2168-2267
PURE: 3236493
https://doi.org/10.1109/TCYB.2016.2621129
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 10
application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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