Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

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  • Zsuzsanna Sükösd, Denmark
  • M Shel Swenson, School of Mathematics, Georgia Institute of Technology, United States
  • Jørgen Kjems
  • Christine E Heitsch, School of Mathematics, Georgia Institute of Technology, United States
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.
Original languageEnglish
JournalNucleic Acids Research
Volume41
Issue5
Pages (from-to)2807-2816
Number of pages10
ISSN0305-1048
DOIs
Publication statusPublished - Mar 2013

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