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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

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