## RNAstructure Command Line Help
Version 5.7

- ### Contents

- ### Index

RNAstructure is a product of the Mathews Lab, University of Rochester Medical Center, Department of Biochemistry and Biophysics.

Continued development of RNAstructure is made possible by the support of NIH grant R01GM076485.

### General Help

- Instructions for building the text interfaces
- General instructions for specifying thermodynamic parameters
- I/O file formats
- Common pathways for analysis, i.e. how the programs work together

### Specific Interface Help

AccessFold
  Bimolecular folding of nucleic acids without intramolecular pairs allowed. This program uses a heuristic to determine accessibility to to duplex formation.
AllSub
  Generate all suboptimal nucleic acid structures within a small free energy increment of the lowest free energy structure.
bifold and bifold-smp
  Bimolecular folding of nucleic acids with intramolecular pairs allowed.
bipartition and bipartition-smp
  Bimolecular partition function calculation of nucleic acids without intramolecular pairs allowed.
CircleCompare
  Compare two structures for the same sequence, with the nucleic acid backbone arranged around a circle to facilitate easy comparisons.
ct2dot
  Generate a dot bracket file from a CT file. The CT file can be regenerated from the dot bracket file using dot2ct (below).
dot2ct
  Generate a CT file from a dot bracket file. The dot bracket file can be regenerated from the CT file using ct2dot (above).
draw
  Draw a structure (or structures) in Postscript from a CT file. This can be done a variety of ways: annotated, unannotated, circularized, or a combination of these.
DuplexFold
  Bimolecular folding of nucleic acids without intramolecular pairs allowed.
dynalign_ii, dynalign, dynalign_ii-smp, and dynalign-smp
  Find a secondary structure common to two sequences.
DynalignDotPlot
  Generate a free energy dot plot from a Dynalign calculation, exported as a Postscript file.
efn2 (Energy Function 2) and efn2-smp
  Determine the folding free energy change of a structure.
EnergyPlot
  Generate a free energy dot plot from a folding calculation save file, exported as a Postscript file.
EnsembleEnergy
  Calculate the ensemble energy of structures from base pair probabilities or sequence data.
Fold and Fold-smp
  Predict the lowest free energy structure for a nucleic acid sequence, as well as a set of low free energy structures.
MaxExpect
  Predict the maximum expected accuracy structure for a nucleic acid sequence.
multifind
  Find non-coding RNAs in sequence alignments.
multilign
  Find secondary structures common to multiple sequences (more than two).
NAPSS
  Use NMR data to improve the prediction of an RNA secondary structure.
oligoscreen and oligoscreen-smp
  Determine folding thermodynamics for a set of oligonucleotides.
OligoWalk
  Calculate thermodynamic features of sense-antisense hybridization and predict free energy changes of oligonucleotides binding to target RNA.
partition and partition-smp
  Predict nucleic acid base pairing probabilities using a partition function.
partition-cuda
  Predict nucleic acid base pairing probabilities using a partition function in parallel using a GPU.
PARTS
  Find a secondary structure common to two nucleic acid sequences, a sample of those structures, and/or the probability of pairing for common base pairs.
phmm
  Predict the probablistic alignment between two RNA sequences.
ProbabilityPlot
  Generate a base pairing probabilities dot plot from a partition function save file, exported as a Postscript file.
ProbablePair
  Predict structures from base pair probabilities, using a threshold to include only pairs within a specific range of probabilities.
ProbKnot
  Predict a maximum expected accuracy structure, including pseudoknots.
refold
  Use a save file to predict a new set of suboptimal structures.
RemovePseudoknots
  Remove pseudoknots from an RNA structure, outputting the most likely pseudoknot-free structure.
scorer
  Calculate sensitivity and positive predictive value for two structures being compared.
ShapeKnots
  Predict a secondary structure that can contains pseudoknots, restrained by SHAPE mapping data.
stochastic and stochastic-smp
  Generate a representative ensemble of structures.
TurboFold
  Fold multiple sequences into their optimal conformations, using one of three different folding modes.