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.
authors: Interdisciplinary Nanoscience Center, Aarhus University, Ny Munkegade 120, Aarhus C DK-8000, Denmark.
authors: Zsuzsanna
authors: Z
authors: Sükösd
authors: M Shel
authors: MS
authors: Swenson
authors: Jørgen
authors: J
authors: Kjems
authors: Christine E
authors: CE
authors: Heitsch
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D016013:Likelihood Functions; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D019642:RNA, Archaeal / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000737:chemistry*; D012337:RNA, Ribosomal, 18S / Q000737:chemistry*; D012984:Software; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S