ProbKnot

[…] have been reported previously., 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., this work used the 2004 set of folding free energy parameters. […]

[…] folding rna structures according to the above golden section points. the sensitivity and number of predicted pseudoknots of our algorithm are better than those of the mfold, hotknots, mcqfold, probknot, and lhw-zhu algorithms. experimental results reflect the folding rules of rna from a new angle that is close to natural folding., rnas are versatile molecules. messenger rnas carry genetic […]

[…] 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, […]

[…] to rna secondary structure analysis via rnastructure version 5.3 . folding was performed using the partition function algorithm, which enables the prediction of putative rna pseudoknots with probknot . we restricted the size of helical regions in the final display to ≥4 base pairs and exported circle plots annotated with base-pair probabilities from the partition function. the 3d […]