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Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions
Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597644/ https://www.ncbi.nlm.nih.gov/pubmed/23325843 http://dx.doi.org/10.1093/nar/gks1283 |
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author | Sükösd, Zsuzsanna Swenson, M. Shel Kjems, Jørgen Heitsch, Christine E. |
author_facet | Sükösd, Zsuzsanna Swenson, M. Shel Kjems, Jørgen Heitsch, Christine E. |
author_sort | Sükösd, Zsuzsanna |
collection | PubMed |
description | Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence. |
format | Online Article Text |
id | pubmed-3597644 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-35976442013-03-15 Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions Sükösd, Zsuzsanna Swenson, M. Shel Kjems, Jørgen Heitsch, Christine E. Nucleic Acids Res Computational Biology Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence. Oxford University Press 2013-03 2013-01-15 /pmc/articles/PMC3597644/ /pubmed/23325843 http://dx.doi.org/10.1093/nar/gks1283 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
spellingShingle | Computational Biology Sükösd, Zsuzsanna Swenson, M. Shel Kjems, Jørgen Heitsch, Christine E. Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions |
title | Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions |
title_full | Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions |
title_fullStr | Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions |
title_full_unstemmed | Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions |
title_short | Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions |
title_sort | evaluating the accuracy of shape-directed rna secondary structure predictions |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597644/ https://www.ncbi.nlm.nih.gov/pubmed/23325843 http://dx.doi.org/10.1093/nar/gks1283 |
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