Multiobjective Metaheuristic to Design RNA Sequences

Detalhes bibliográficos
Autor(a) principal: Rubio-Largo, Álvaro
Data de Publicação: 2019
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/10362/146177
Resumo: Rubio-Largo, A., Vanneschi, L., Castelli, M., & Vega-Rodriguez, M. A. (2019). Multiobjective Metaheuristic to Design RNA Sequences. IEEE Transactions on Evolutionary Computation, 23(1). DOI: 10.1109/TEVC.2018.2844116
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spelling Multiobjective Metaheuristic to Design RNA SequencesInverse foldingMetaheuristicMultiobjective optimizationRNASoftwareTheoretical Computer ScienceComputational Theory and MathematicsSDG 3 - Good Health and Well-beingRubio-Largo, A., Vanneschi, L., Castelli, M., & Vega-Rodriguez, M. A. (2019). Multiobjective Metaheuristic to Design RNA Sequences. IEEE Transactions on Evolutionary Computation, 23(1). DOI: 10.1109/TEVC.2018.2844116RNA inverse folding problem is a bioinformatics problem where the objective is to find an RNA sequence that folds into a given target secondary structure. In this work, we use Evolutionary Computation to solve a new and innovative multiobjective definition of this problem. In this new multiobjective definition of the problem, we have considered the similarity between target and predicted structures as a constraint, and three objective functions: (i) Partition Function (free energy of the ensemble), (ii) Ensemble Diversity and (iii) Nucleotides Composition. The Multiobjective Metaheuristic To Design RNA Sequences (m2dRNAs) proposed in this paper is compared against other RNA inverse folding methods published in the literature, such as RNAinverse, RNA-SSD, INFO-RNA, MODENA, NUPACK, fRNAkenstein, DSS-Opt, RNAiFOLD, antaRNA, ERD, and Eterna players. After a comprehensive comparative study on two well-known benchmarks (Rfam and Eterna100), we conclude that m2dRNAs is capable of obtaining very promising results in terms of both quality of RNA designs and required runtime. The source code of m2dRNAs is available at http://arco.unex.es/arl/m2dRNAs-sourcecode.zip.NOVA Information Management School (NOVA IMS)Information Management Research Center (MagIC) - NOVA Information Management SchoolRUNRubio-Largo, ÁlvaroVanneschi, LeonardoCastelli, MauroVega-Rodriguez, Miguel A.2022-12-13T22:06:56Z2019-022019-02-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article14application/pdfhttp://hdl.handle.net/10362/146177eng1089-778XPURE: 4364927https://doi.org/10.1109/TEVC.2018.2844116info: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:RCAAP2024-03-11T05:27:13Zoai:run.unl.pt:10362/146177Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:52:31.522972Repositório 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 Multiobjective Metaheuristic to Design RNA Sequences
title Multiobjective Metaheuristic to Design RNA Sequences
spellingShingle Multiobjective Metaheuristic to Design RNA Sequences
Rubio-Largo, Álvaro
Inverse folding
Metaheuristic
Multiobjective optimization
RNA
Software
Theoretical Computer Science
Computational Theory and Mathematics
SDG 3 - Good Health and Well-being
title_short Multiobjective Metaheuristic to Design RNA Sequences
title_full Multiobjective Metaheuristic to Design RNA Sequences
title_fullStr Multiobjective Metaheuristic to Design RNA Sequences
title_full_unstemmed Multiobjective Metaheuristic to Design RNA Sequences
title_sort Multiobjective Metaheuristic to Design RNA Sequences
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 Inverse folding
Metaheuristic
Multiobjective optimization
RNA
Software
Theoretical Computer Science
Computational Theory and Mathematics
SDG 3 - Good Health and Well-being
topic Inverse folding
Metaheuristic
Multiobjective optimization
RNA
Software
Theoretical Computer Science
Computational Theory and Mathematics
SDG 3 - Good Health and Well-being
description Rubio-Largo, A., Vanneschi, L., Castelli, M., & Vega-Rodriguez, M. A. (2019). Multiobjective Metaheuristic to Design RNA Sequences. IEEE Transactions on Evolutionary Computation, 23(1). DOI: 10.1109/TEVC.2018.2844116
publishDate 2019
dc.date.none.fl_str_mv 2019-02
2019-02-01T00:00:00Z
2022-12-13T22:06:56Z
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/10362/146177
url http://hdl.handle.net/10362/146177
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1089-778X
PURE: 4364927
https://doi.org/10.1109/TEVC.2018.2844116
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 14
application/pdf
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instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
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