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RNAstructure GUI Help
Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z


A

About RNAstructure
Accuracy
Acknowledgements
Algorithm
Alignment File Format
Annotating a Structure
Asking for Help
Audio Playback

N

B

Breaking Pseudoknots
Bulge Loop Size

O

OligoScreen
OligoScreen Thermodynamic Parameters
OligoWalk
OligoWalk Calculations
OligoWalk Modes
OligoWalk Results
OligoWalk Thermodynamic Parameters
Outputting Base Pair Probabilities
Overview

C

Calculating Stochastic Samples
Calculation Modules
Changing Temperature of Calculations
Constraint File Format
Creating a Sequence
CT File Format

P

Partition Function
Partition Function Bimolecular
Partition Function Dot Plots
Plot Range
Postscript Output
Precision
Predicting Base Pair Probabilities
Predicting Pseudoknots
Prediction Modules
Printing a Structure
Probability Annotation
ProbKnot
Pseudo-Energy Constraints (SHAPE)
Pseudoknots
Publication Quality Output

D

DH Thermodynamic Parameters
DNA Menu
DNA Thermodynamic Parameters
DNA-RNA Thermodynamic Parameters
Dot Plot Appearance
Dot Plot Color Selection
Dot Plot Module
Double Stranded Bases
Draw Module
Drawing a Structure
DS Thermodynamic Parameters
Dynalign Dot Plots
Dynalign Thermodynamic Parameters

Q

Quick Access Toolbar

E

Editing a Sequence
Efn2 (Energy Function 2)
Enthalpy Thermodynamic Parameters

R

Read While Typing
Refold
Refolding Dynalign Calculations
Refolding Structures
Rendering a Structure by Direction
Report a Bug
Resetting Constraints
Restoring Constraints
Reviewing Constraints
RNA Menu

F

FASTA File Format
File Formats
File Menu
Folding Dot Plots
Forbidding a Base Pair
Forcing a Base Pair
Forcing Double Stranded Bases
Forcing Single Stranded Bases
Formatting a Sequence
Free Energy Calculation
Free Energy Thermodynamic Parameters

S

Saving Constraints
Sequence Entry Particulars
Sequence File Format
SHAPE Annotation
SHAPE Constraints
SHAPE File Format
Single Stranded Bases
Specifying Chemical Modification
Specifying FMN Cleavage
Stochastic Sampling
StructureEditor
Support
Switching Between Structures
System Requirements

G

Generating Suboptimal Structures

T

Thermodynamic Parameters
Toolbar

H

Hard Constraints (SHAPE)
Help Menu

U

Using Calculation Constraints
Using OligoScreen
Using OligoWalk

I

Image Output
Internal Loop Size

V

Variable Menus
Viewing an Entire Structure

J

W

K

X

L

List File Format
Loading a Sequence

Y

M

Making Suggestions
Maximum Expected Accuracy
Module List

Z

Zooming a Structure