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Table 1 Single Sequence Methods.

From: RNAstructure: software for RNA secondary structure prediction and analysis

Feature: Text Interface Program: JAVA/Windows GUI Menu Item: Class Library and Function Name:
Free energy minimization structure prediction [14] Fold Fold RNA
Single Strand
RNA::FoldSingleStrand
Maximum expected accuracy structure prediction [18] MaxExpect Predict
Maximum
Expected
Accuracy
Structure
RNA:MaximizeExpectedAccuracy
Partition function [22] partition Partition
Function RNA
RNA::PartitionFunction
Efn2 (energy calculator) [13] efn2 Efn2 RNA RNA:: CalculateFreeEnergy
Free energy minimization and generation of all suboptimal structures [28, 47] AllSub Generate All
Suboptimal
RNA Structures
RNA::GenerateAllSuboptimalStructures
Stochastic sampling of structures [17] stochastic Stochastic RNA
Sampling
RNA::Stochastic
Remove Pseudoknots [49] RemovePseudoknots Break
Pseudoknots
RNA::BreakPeudoknots
Prediction of structures with pairs above specified pairing probability threshold [22] ProbablePair Output Probable
Structure
RNA::PredictProbablePairs
Drawing secondary structure diagrams draw Draw RNA::DetermineDrawingCoordinates
NAPSS [30] NAPSS - -