Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools

Detalhes bibliográficos
Autor(a) principal: Antunes, Deborah
Data de Publicação: 2017
Outros Autores: Jorge, Natasha Andressa Nogueira, Caffarena, Ernesto Raul, Passetti, Fabio
Tipo de documento: Artigo
Idioma: por
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/38728
Resumo: Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.
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spelling Antunes, DeborahJorge, Natasha Andressa NogueiraCaffarena, Ernesto RaulPassetti, Fabio2019-12-19T17:56:28Z2019-12-19T17:56:28Z2017ANTUNES, Deborah et al. Using RNA sequence and structure for the prediction of riboswitch aptamer: a comprehensive review of available software and tools. Frontiers in Genetics, v. 8, n. 231, p. 1-16, 2019.1664-8021https://www.arca.fiocruz.br/handle/icict/3872810.3389/fgene.2017.002311664-8021porFrontiers MediaRiboswitchMoléculas RNANucleotide MotifsRNA moleculesMotivos de NucleótidosMotivos de NucleotídeosUsing RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and toolsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Regulação da Expressão Gênica. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Regulação da Expressão Gênica. Curitiba, PR, Brasil.RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles. Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates. However, to date, only a few approaches have been developed for the computational prediction of RNA structures. Similar to proteins, RNA structures may be altered due to the interaction with various ligands, including proteins, other RNAs, and metabolites. A riboswitch is a molecular mechanism, found in the three kingdoms of life, in which the RNA structure is modified by the binding of a metabolite. It can regulate multiple gene expression mechanisms, such as transcription, translation initiation, and mRNA splicing and processing. Due to their nature, these entities also act on the regulation of gene expression and detection of small metabolites and have the potential to helping in the discovery of new classes of antimicrobial agents. In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83084https://www.arca.fiocruz.br/bitstream/icict/38728/1/license.txt783568c2893d2e25a99990b126be1772MD51ORIGINALfgene-08-00231ok.pdffgene-08-00231ok.pdfapplication/pdf7196850https://www.arca.fiocruz.br/bitstream/icict/38728/2/fgene-08-00231ok.pdf1f502d16534e6bca581e7ecc77550717MD52TEXTfgene-08-00231ok.pdf.txtfgene-08-00231ok.pdf.txtExtracted texttext/plain88388https://www.arca.fiocruz.br/bitstream/icict/38728/3/fgene-08-00231ok.pdf.txt4b3c7945866fba46a8571436120a92feMD53icict/387282021-12-13 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dc.title.pt_BR.fl_str_mv Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
title Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
spellingShingle Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
Antunes, Deborah
Riboswitch
Moléculas RNA
Nucleotide Motifs
RNA molecules
Motivos de Nucleótidos
Motivos de Nucleotídeos
title_short Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
title_full Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
title_fullStr Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
title_full_unstemmed Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
title_sort Using RNA sequence and structure for the prediction of riboswitch aptamer: A comprehensive review of available software and tools
author Antunes, Deborah
author_facet Antunes, Deborah
Jorge, Natasha Andressa Nogueira
Caffarena, Ernesto Raul
Passetti, Fabio
author_role author
author2 Jorge, Natasha Andressa Nogueira
Caffarena, Ernesto Raul
Passetti, Fabio
author2_role author
author
author
dc.contributor.author.fl_str_mv Antunes, Deborah
Jorge, Natasha Andressa Nogueira
Caffarena, Ernesto Raul
Passetti, Fabio
dc.subject.other.pt_BR.fl_str_mv Riboswitch
Moléculas RNA
topic Riboswitch
Moléculas RNA
Nucleotide Motifs
RNA molecules
Motivos de Nucleótidos
Motivos de Nucleotídeos
dc.subject.en.pt_BR.fl_str_mv Nucleotide Motifs
RNA molecules
dc.subject.es.pt_BR.fl_str_mv Motivos de Nucleótidos
dc.subject.decs.pt_BR.fl_str_mv Motivos de Nucleotídeos
description Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Biofísica Computacional e Modelagem Molecular. Rio de Janeiro, RJ, Brasil.
publishDate 2017
dc.date.issued.fl_str_mv 2017
dc.date.accessioned.fl_str_mv 2019-12-19T17:56:28Z
dc.date.available.fl_str_mv 2019-12-19T17:56:28Z
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.citation.fl_str_mv ANTUNES, Deborah et al. Using RNA sequence and structure for the prediction of riboswitch aptamer: a comprehensive review of available software and tools. Frontiers in Genetics, v. 8, n. 231, p. 1-16, 2019.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/38728
dc.identifier.issn.pt_BR.fl_str_mv 1664-8021
dc.identifier.doi.none.fl_str_mv 10.3389/fgene.2017.00231
dc.identifier.eissn.none.fl_str_mv 1664-8021
identifier_str_mv ANTUNES, Deborah et al. Using RNA sequence and structure for the prediction of riboswitch aptamer: a comprehensive review of available software and tools. Frontiers in Genetics, v. 8, n. 231, p. 1-16, 2019.
1664-8021
10.3389/fgene.2017.00231
url https://www.arca.fiocruz.br/handle/icict/38728
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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