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RNAstructure Installation and Overview
Repository Organization

Code Directories

Directory Description
RNA_class A group of related object wrappers that encapsulate most back end code for easy use
src Location of most back end code

GUI Directories

Directory Description
java_interface Cross-platform Java interface capable of running on Linux, Mac, or Windows operating systems

Text Interface Directories

Directory Description
AllSub Generate a group of suboptimal structures
bifold Bimolecular folding
bipartition Bimolecular partition function for predicting pair probabilities
CircleCompare Compare two structures for the same sequence, with the nucleic acid backbone arranged around a circle to facilitate easy comparisons
ct2dot Convert CT structure notation to dot bracket structure notation
designFind an RNA (or DNA) sequence that is expected to fold into a given structure.
dot2ct Convert dot bracket structure notation to CT structure notation
DotPlots Creates three separate interfaces that can make different dot plot types
draw Generate Postscript images of secondary structures
DuplexFold Bimolecular folding without intramolecular pairs
dynalign Predict the lowest free energy structure common to two sequences
efn2 Predict folding free energy change of a given structure
EnsembleEnergy Predict the energy of a structure ensemble.
fold Single sequence secondary structure prediction by free energy minimization
MaxExpect Secondary structure prediction by maximizing expected accuracy
multilign Predict the lowest free energy structure common to more than two sequences
napss Use NMR data to improve the prediction of an RNA secondary structure
oligoscreen Screen a set of oligonuceotides for hybridization stability and self-structure
oligowalk Calculate thermodynamic features of sense-antisense hybridization and predict free energy changes of oligo binding to target RNA
PARTS Predict pair probabilities for folding of two sequences to a common structure
pfunction Partition function calculation of base pairing probabilities
ProbablePair Generate structures composed of only highly probable pairs as determined by a threshold
ProbKnot Predict pseudoknots for a single sequence
refold Refold a previously folded structure
RemovePseudoknots Remove pseudoknots from a structure
Windows_text_interfaces Visual Studio Project files for editing and building the Text interfaces on Windows
scorer Calculate sensitivity and positive predictive value for two structures being compared
stochastic Stochastic sampling from the Boltzman ensemble
TurboFold Predict the lowest free energy structure common to more than two sequences, using base pairing probabilities.

Resource Directories

Directory Description
data_tables Location of thermodynamic parameters
exe Holds executables for text interfaces, GUIs, and any libraries
tests Project tests for each text interface

Help Directories

Directory Description
examples Sample input files
manual Help and some usage documentation

Essential Top-Level Files

File Name Description
compiler.h Compiler and compilation flags, macros, and definitions
gpl.txt The GPL license under which the RNAstructure software package falls
library_defines.h Names for the libraries the repository builds, defined by operating system
Makefile The main Makefile which builds most of the repository modules
Version.txt Contains the most recent version number and release date for the repository