RNAstructure

Version 5.1

Copyright 1996 - 2010

by David H. Mathews


Available Modules for Prediction and Calculation

Break RNA Pseudoknots

This item, unique to RNA, unravels pseudoknots in RNA primary sequence to allow for easier calculation of secondary 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. Note, however, that the drawing may not display properly if the structure contains pseudoknots. 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 folding algorithm similar to mfold. 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."


Maximum Expected Accuracy

This item predicts a specific subset of structures composed of probable base pairs and single-stranded nucleotides. See "Maximum Expected Accuracy".


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 which 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

This item will calculate probable 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".