Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions
| Autor: | Zsuzsanna Sükösd, M. Shel Swenson, Christine E. Heitsch, Jørgen Kjems |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular Stochastic modelling RNA Archaeal Biology Bioinformatics Nucleic acid secondary structure Set (abstract data type) Correlation 03 medical and health sciences 0302 clinical medicine RNA Ribosomal 16S Genetics RNA Ribosomal 18S Animals Computer Simulation 030304 developmental biology 0303 health sciences Sequence Likelihood Functions Stochastic Processes Stochastic process Computational Biology Predictive value RNA Bacterial Test sequence Nucleic Acid Conformation Thermodynamics Algorithm 030217 neurology & neurosurgery Algorithms Software |
| Zdroj: | Sükösd, Z, Swenson, M S, Kjems, J & Heitsch, C E 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 Nucleic Acids Research |
| DOI: | 10.1093/nar/gks1283 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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