ProbKnot

[…] to compose a structure with base pairs with estimated base pairing probabilities higher than threshold, using the maximum expected accuracy (MEA) secondary structure prediction algorithm (–), or the ProbKnot method (,). TurboFold is iterative, with the extrinsic information being updated with each iteration, and the iterations were shown to improve the accuracy of the base pairing probability est […]

[…] Calculations were performed using the RNAstructure package (). Specifically, partition function (program partition) (), stochastic sampling (program stochastic), ProbKnot (), secondary structure comparison (program scorer) and the folding free energy calculator (program efn2) were used. […]

[…] esis (H0), stating that NAPSS-CS is not more accurate than an alternative program, was tested. Constrained NAPSS-CS was found to have a sensitivity (p < 0.05) significantly higher than those of Fold, ProbKnot, and ShapeKnots, and a PPV significantly higher than that of ProbKnot ().For structures with pseudoknots, the sensitivity and PPV for pseudoknotted base pairs were calculated separately with […]

[…] ich includes 47 sequences from PseudoBase and PDB, which is also a subset of those used in the HotKnots.We present the prediction results of our method compared with those of HotKnots [], McQfold [], ProbKnot [], TT2NE [], Mfold [], and LZ []. MFold is restricted to secondary structures that are free of pseudoknots, whereas others can result in any topology of pseudoknot.This set includes most of […]

[…] prediction for sequences of this size and most likely substantially larger.We also used the calculated base pair probabilities to determine a single consensus structure for each sequences, using the ProbKnot algorithm []. In this case, working in single precision led to differences with double precision only for one sequence (a random sequence of 6000 bases) out of the 44 we examined, and these w […]

[…] all predictions for those sequences in the RNAstrand data set, for which CompaRNA managed to assign an Rfam family—apart from ContextFold and UNAFold, these were IPknot, Contrafold, Sfold, MaxExpect, ProbKnot, Fold and RNAfold. The most robust comparative method turned out to be MXScarna—when run with a query comprising all sequences from the Rfam seed alignment, it generated predictions for 36.6% […]