| ## RNAstructure GUI Help Available Modules for Prediction and Calculation | ### Contents ### Index
Break RNA Pseudoknots This item, unique to RNA, breaks pseudoknots in an RNA secondary structure, leaving a pseudoknot-free structure. See "Break RNA Pseudoknots." Dot Plot This item allows the display of a dot plot using one of many save file types generated from various manipulations of a sequence. See "Dot Plot." Draw This item will draw any structure saved in the CT file format. See "Draw." Dynalign This item opens the Dynalign tool, which will find the sequence alignment and the lowest free energy common structure common to two sequences. See "Dynalign." Efn2 This item will determine the free energy of a secondary structure saved in the CT file format. See "Efn2." Fold Single Strand This item will open a folding window. This is the traditional structure prediction algorithm that finds lowest free energy structures. See "Fold." Fold Bimolecular This item will predict the intermolecular secondary structures of two oligonucleotides. See "Fold -> Bimolecular Folding." Generate All Suboptimal Structures This item allows the prediction of all possible secondary structures within a specified energy increment of the lowest free energy structure. See "Generate All Suboptimal Structures." MaxExpect: Predict MEA Structure This item predicts maximum expected accuracy structures, which are structures composed of the most probable pairs. See "Maximum Expected Accuracy." Multilign This item predicts common secondary structures for multiple sequences (more than two). See "Multilign." OligoScreen This item opens the OligoScreen tool, which determines thermodynamic parameters for a set of oligonucleotides. See "OligoScreen." OligoWalk This item opens the OligoWalk tool, which can help to determine an oligomer that will hybridize tightly to a target. See "OligoWalk." Partition Function This item uses a partition function calculation to predict base pair probabilities for any canonical pair in the sequence. See "Partition Function." Partition Function Bimolecular This item uses a partition function calculation to predict base pair probabilities for base pairs between two sequences. See "Partition Function -> Bimolecular Partitioning." ProbKnot: Predict Structures Including Pseudoknots This item will predict a maximum expected accuracy structure, including pseudoknots, from a partition function save file, and save the result as a CT file. See "ProbKnot." Refold This item can be used to predict a different set of suboptimal secondary structures from a previously folded sequence or calculation. See "Refold." Stochastic Sampling This item generates a sample of secondary structures for a sequence, drawn from the complete folding ensemble. See "Stochastic Sampling." TurboFold This item predicts common secondary structures for multiple sequences (more than two) using base pairing probabilities. See "TurboFold."