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

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  • dc.contributor.author Garcia-Martin, Juan Antonioca
  • dc.contributor.author Dotu, Ivanca
  • dc.contributor.author Clote, Peterca
  • dc.date.accessioned 2015-11-18T09:47:30Z
  • dc.date.available 2015-11-18T09:47:30Z
  • dc.date.issued 2015
  • dc.description.abstract 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.ca
  • dc.description.sponsorship National Science Foundation [DBI-1262439]. Funding for open access charge: National Science Foundation./nConflict of interest statement. None declared.
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Garcia-Martin JA, Dotu I, Clote P. RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. Nucleic Acids Res. 2015 Jul 1;43(W1):W513-21. DOI: 10.1093/nar/gkv460.ca
  • dc.identifier.doi http://dx.doi.org/10.1093/nar/gkv460
  • dc.identifier.issn 0305-1048
  • dc.identifier.uri http://hdl.handle.net/10230/25130
  • dc.language.iso engca
  • dc.publisher Oxford University Pressca
  • dc.relation.ispartof Nucleic Acids Research. 2015 Jul 1;43(W1):W513-21
  • dc.rights © 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.comca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/),/ca
  • dc.subject.other Molècules -- Models -- Simulació per ordinadorca
  • dc.title RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.ca
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

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