RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.

Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead...

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Detalles Bibliográficos
Autores: Garcia-Martin, Juan Antonio, Dotu, Ivan, Clote, Peter
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2015
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/25130
Acceso en línea:http://hdl.handle.net/10230/25130
http://dx.doi.org/10.1093/nar/gkv460
Access Level:acceso abierto
Palabra clave:Molècules -- Models -- Simulació per ordinador
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spelling RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.Garcia-Martin, Juan AntonioDotu, IvanClote, PeterMolècules -- Models -- Simulació per ordinadorSeveral algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules.National Science Foundation [DBI-1262439]. Funding for open access charge: National Science Foundation./nConflict of interest statement. None declared.Oxford University Press201520152015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/25130http://dx.doi.org/10.1093/nar/gkv460reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésNucleic Acids Research. 2015 Jul 1;43(W1):W513-21© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comhttp://creativecommons.org/licenses/by-nc/4.0/),/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/251302026-05-29T05:05:01Z
dc.title.none.fl_str_mv RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
title RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
spellingShingle RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
Garcia-Martin, Juan Antonio
Molècules -- Models -- Simulació per ordinador
title_short RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
title_full RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
title_fullStr RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
title_full_unstemmed RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
title_sort RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
dc.creator.none.fl_str_mv Garcia-Martin, Juan Antonio
Dotu, Ivan
Clote, Peter
author Garcia-Martin, Juan Antonio
author_facet Garcia-Martin, Juan Antonio
Dotu, Ivan
Clote, Peter
author_role author
author2 Dotu, Ivan
Clote, Peter
author2_role author
author
dc.subject.none.fl_str_mv Molècules -- Models -- Simulació per ordinador
topic Molècules -- Models -- Simulació per ordinador
description Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/25130
http://dx.doi.org/10.1093/nar/gkv460
url http://hdl.handle.net/10230/25130
http://dx.doi.org/10.1093/nar/gkv460
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nucleic Acids Research. 2015 Jul 1;43(W1):W513-21
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc/4.0/),/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/4.0/),/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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