A folding algorithm for extended RNA secondary structures

Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. Results: We pres...

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Detalles Bibliográficos
Autores principales: zu Siederdissen, Christian Höner, Bernhart, Stephan H., Stadler, Peter F., Hofacker, Ivo L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Ismb/Eccb 2011 Proceedings Papers Committee July 17 to July 19, 2011, Vienna, Austria
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117358/
https://www.ncbi.nlm.nih.gov/pubmed/21685061
http://dx.doi.org/10.1093/bioinformatics/btr220
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author zu Siederdissen, Christian Höner
Bernhart, Stephan H.
Stadler, Peter F.
Hofacker, Ivo L.
author_facet zu Siederdissen, Christian Höner
Bernhart, Stephan H.
Stadler, Peter F.
Hofacker, Ivo L.
author_sort zu Siederdissen, Christian Höner
collection PubMed
description Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/. Contact: choener@tbi.univie.ac.at
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spelling pubmed-31173582011-06-17 A folding algorithm for extended RNA secondary structures zu Siederdissen, Christian Höner Bernhart, Stephan H. Stadler, Peter F. Hofacker, Ivo L. Bioinformatics Ismb/Eccb 2011 Proceedings Papers Committee July 17 to July 19, 2011, Vienna, Austria Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/. Contact: choener@tbi.univie.ac.at Oxford University Press 2011-07-01 2011-06-14 /pmc/articles/PMC3117358/ /pubmed/21685061 http://dx.doi.org/10.1093/bioinformatics/btr220 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Ismb/Eccb 2011 Proceedings Papers Committee July 17 to July 19, 2011, Vienna, Austria
zu Siederdissen, Christian Höner
Bernhart, Stephan H.
Stadler, Peter F.
Hofacker, Ivo L.
A folding algorithm for extended RNA secondary structures
title A folding algorithm for extended RNA secondary structures
title_full A folding algorithm for extended RNA secondary structures
title_fullStr A folding algorithm for extended RNA secondary structures
title_full_unstemmed A folding algorithm for extended RNA secondary structures
title_short A folding algorithm for extended RNA secondary structures
title_sort folding algorithm for extended rna secondary structures
topic Ismb/Eccb 2011 Proceedings Papers Committee July 17 to July 19, 2011, Vienna, Austria
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117358/
https://www.ncbi.nlm.nih.gov/pubmed/21685061
http://dx.doi.org/10.1093/bioinformatics/btr220
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