Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Standard

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. / Sükösd, Zsuzsanna; Swenson, M Shel; Kjems, Jørgen; Heitsch, Christine E.

In: Nucleic Acids Research, Vol. 41, No. 5, 03.2013, p. 2807-2816.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Sükösd, Z, Swenson, MS, Kjems, J & Heitsch, CE 2013, 'Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions', Nucleic Acids Research, vol. 41, no. 5, pp. 2807-2816. https://doi.org/10.1093/nar/gks1283

APA

Sükösd, Z., Swenson, M. S., Kjems, J., & Heitsch, C. E. (2013). Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Research, 41(5), 2807-2816. https://doi.org/10.1093/nar/gks1283

CBE

Sükösd Z, Swenson MS, Kjems J, Heitsch CE. 2013. Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Research. 41(5):2807-2816. https://doi.org/10.1093/nar/gks1283

MLA

Sükösd, Zsuzsanna et al. "Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions". Nucleic Acids Research. 2013, 41(5). 2807-2816. https://doi.org/10.1093/nar/gks1283

Vancouver

Sükösd Z, Swenson MS, Kjems J, Heitsch CE. Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. Nucleic Acids Research. 2013 Mar;41(5):2807-2816. https://doi.org/10.1093/nar/gks1283

Author

Sükösd, Zsuzsanna ; Swenson, M Shel ; Kjems, Jørgen ; Heitsch, Christine E. / Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. In: Nucleic Acids Research. 2013 ; Vol. 41, No. 5. pp. 2807-2816.

Bibtex

@article{1545884263fb48718646e2ca54bf17f6,
title = "Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions",
abstract = "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.",
author = "Zsuzsanna S{\"u}k{\"o}sd and Swenson, {M Shel} and J{\o}rgen Kjems and Heitsch, {Christine E}",
year = "2013",
month = "3",
doi = "10.1093/nar/gks1283",
language = "English",
volume = "41",
pages = "2807--2816",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "5",

}

RIS

TY - JOUR

T1 - Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

AU - Sükösd, Zsuzsanna

AU - Swenson, M Shel

AU - Kjems, Jørgen

AU - Heitsch, Christine E

PY - 2013/3

Y1 - 2013/3

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gks1283

DO - 10.1093/nar/gks1283

M3 - Journal article

C2 - 23325843

VL - 41

SP - 2807

EP - 2816

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 5

ER -