Table 1.
Single Sequence Methods.
| 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 | - | - |