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 | - | - |