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Characterising RNA secondary structure space using information entropy

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is,...

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Detalles Bibliográficos
Autores principales: Sükösd, Zsuzsanna, Knudsen, Bjarne, Anderson, James WJ, Novák, Ádám, Kjems, Jørgen, Pedersen, Christian NS
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549843/
https://www.ncbi.nlm.nih.gov/pubmed/23368905
http://dx.doi.org/10.1186/1471-2105-14-S2-S22
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author Sükösd, Zsuzsanna
Knudsen, Bjarne
Anderson, James WJ
Novák, Ádám
Kjems, Jørgen
Pedersen, Christian NS
author_facet Sükösd, Zsuzsanna
Knudsen, Bjarne
Anderson, James WJ
Novák, Ádám
Kjems, Jørgen
Pedersen, Christian NS
author_sort Sükösd, Zsuzsanna
collection PubMed
description Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/.
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spelling pubmed-35498432013-05-22 Characterising RNA secondary structure space using information entropy Sükösd, Zsuzsanna Knudsen, Bjarne Anderson, James WJ Novák, Ádám Kjems, Jørgen Pedersen, Christian NS BMC Bioinformatics Proceedings Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/. BioMed Central 2013-01-21 /pmc/articles/PMC3549843/ /pubmed/23368905 http://dx.doi.org/10.1186/1471-2105-14-S2-S22 Text en Copyright © 2013 Sükösd et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Sükösd, Zsuzsanna
Knudsen, Bjarne
Anderson, James WJ
Novák, Ádám
Kjems, Jørgen
Pedersen, Christian NS
Characterising RNA secondary structure space using information entropy
title Characterising RNA secondary structure space using information entropy
title_full Characterising RNA secondary structure space using information entropy
title_fullStr Characterising RNA secondary structure space using information entropy
title_full_unstemmed Characterising RNA secondary structure space using information entropy
title_short Characterising RNA secondary structure space using information entropy
title_sort characterising rna secondary structure space using information entropy
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549843/
https://www.ncbi.nlm.nih.gov/pubmed/23368905
http://dx.doi.org/10.1186/1471-2105-14-S2-S22
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