## RNAstructure Installation and Overview
Software Package Components

- ### Contents

- ### Index

## Single Sequence Methods

Feature | Text Interface Program | JAVA/Windows GUI Menu Item | Class Library and Function Name
--- | --- | --- | ---
Free energy minimization and generation of all suboptimal structures (References: Duan et al. 2006, Wuchty et al. 1999) | AllSub | Generate All Suboptimal RNA Structures | RNA::GenerateAllSuboptimalStructures
Drawing secondary structure diagrams | draw | Draw | RNA::DetermineDrawingCoordinates
Efn2 (Energy function 2) (Reference: Mathews, Sabina et al. 1999) | efn2 | Efn2 RNA | RNA::CalculateFreeEnergy
Free energy minimization structure prediction (Reference: Mathews et al. 2004) | Fold | Fold RNA Single Strand | RNA::FoldSingleStrand
Maximum expected accuracy structure prediction (Reference: Lu et al. 2009) | MaxExpect | MaxExpect: Predict RNA MEA Structure | RNA::MaximumExpectedAccuracy
NAPSS (Reference: Hart et al. 2008) | NAPSS | N/A | N/A
Partition function (Reference: Mathews 2004) | partition | Partition Function RNA | RNA::PartitionFunction
Partition function, implemented in parallel for CUDA GPUs | partition-cuda | N/A | N/A
Prediction of structures with pairs above specified pairing probability threshold (Reference: Mathews 2004) | ProbablePair | Output Probable Structures | RNA::PredictProbablePairs
Prediction of secondary structures including pseudoknots (Reference: Bellaousov and Mathews 2010) | ProbKnot | ProbKnot: Predict RNA MEA Structure Including Pseudoknots | RNA::ProbKnot
Remove Pseudoknots Reference: (Smit et al. 2008) | RemovePseudoknots | Break Pseudoknots | RNA::BreakPseudoknot
Predict structures that may contains pseudoknots, restrained by SHAPE mapping data. | ShapeKnots | N/A | N/A
Stochastic sampling of structures (Reference: Ding and Lawrence, 2003) | stochastic | Stochastic RNA Sampling | RNA::Stochastic

## Multiple Sequence Methods (Bimolecular or Common Folding)

Feature | Text Interface Program | JAVA/Windows GUI Menu Item | Class Library and Function Name
--- | --- | --- | ---
Bimolecular structure prediction with intramolecular pairs | bifold | Fold RNA Bimolecular | HybridRNA::FoldBimolecular
Bimolecular partition function (no intramolecular pairs) | bipartition | Partition Function RNA Bimolecular | HybridRNA::PartitionFunctionBimolecular
Bimolecular structure prediction without intramolecular pairs | DuplexFold | N/A | HybridRNA::FoldDuplex
Dynalign (References: Harmanci et al. 2007, Uzilov et al 2006, Mathews and Turner 2002) | dynalign | RNA Dynalign | Dynalign_object::Dynalign
Dynalign II | dynalign_ii | N/A | Dynalign_object::Dynalign (Built by defining DYNALIGN_II at precompile time)
Multilign (Reference: Xu and Mathews, 2011) | multilign | RNA Multilign | Multilign_object::ProgressiveMultilign
OligoScreen Reference: Mateeva et al. 2003) | oligoscreen | OligoScreen | Oligowalk_object::OligoScreen
OligoWalk (References: Lu and Mathews, 2008, Lu and Mathews, 2007, Mathews, Burkard et al. 1999) | OligoWalk | OligoWalk | Oligowalk_object::OligoWalk
PARTS (References: Harmanci et al. 2009, Harmanci et al. 2008) | PARTS | N/A | N/A
TurboFold References: Harmanci et al. 2011) | TurboFold | RNA TurboFold | TurboFold::fold

## Utilities

Feature | Text Interface Program | JAVA/Windows GUI Menu Item | Class Library and Function Name
--- | --- | --- | ---
Circular structure comparison | CircleCompare | N/A | N/A
CT file to dot bracket file conversion | ct2dot | N/A | N/A
Dot bracket file to CT file conversion | dot2ct | N/A | N/A
Create a dot plot from a Dynalign save file | DynalignDotPlot | Dot Plot Dynalign | N/A
Create a dot plot from a folding energy save file | EnergyPlot | Dot Plot | N/A
Ensemble energy calculation | EnsembleEnergy | N/A | N/A
Create a dot plot from a partition function save file | ProbabilityPlot | Dot Plot Partition Function | N/A
Refold from a previously folded sequence. | refold | Refold From Save File | RNA::ReFoldSingleStrand
Scoring comparison of two structures (Reference: Mathews, Sabina et al. 1999) | scorer | N/A | N/A

### References

1. Harmanci, A.O., Sharma, G. and Mathews, D.H. (2011).
   TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences.
   BMC Bioinformatics. 12:108.
2. Xu, Z., and Mathews, D.H. (2011).
   Multilign: An algorithm to predict secondary structures conserved in multiple RNA sequences.
   Bioinformatics, 27:626-632.
3. Bellaousov, S., and Mathews, D. H. (2010.
   ProbKnot: fast prediction of RNA secondary structure including pseudoknots.
   RNA. 16:1870-1880.
4. Harmanci, A.O., Sharma, G. and Mathews, D.H. (2009).
   Stochastic sampling of the RNA structural alignment space.
   Nucleic Acids Res., 37:4063-4075.
5. Lu, Z.J., Gloor, J.W. and Mathews, D.H. (2009).
   Improved RNA Secondary Structure Prediction by Maximizing Expected Pair Accuracy.
   RNA, 15:1805-1813.
6. Harmanci, A.O., Sharma, G. and Mathews, D.H. (2008).
   PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction.
   Nucleic Acids Res., 36:2406-2417.
7. Hart, J.M., Kennedy, S.D., Mathews, D.H. and Turner, D.H. (2008).
   NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.
   J. Am. Chem. Soc., 130:10233-10239.
8. Lu, Z.J. and Mathews, D.H. (2008).
   Fundamental Differences in the Equilibrium Considerations for siRNA and Antisense Oligodeoxynucleotide Design.
   Nucleic Acids Res., 36:3738-3745.
9. Smit, S., Rother, K., Heringa, J. and Knight, R. (2008).
   From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
   RNA, 14:410-416.
10. Harmanci, A.O., Sharma, G. and Mathews, D.H. (2007).
    Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign.
    BMC Bioinformatics, 8:130.
11. Lu, Z.J. and Mathews, D.H. (2007).
    Efficient siRNA Selection Using Hybridization Thermodynamics.
    Nucleic Acids Res., 36:640-647.
12. Duan, S., Mathews, D.H. and Turner, D.H. (2006).
    Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.
    Biochemistry, 45:9819-9832.
13. Uzilov, A.V., Keegan, J.M. and Mathews, D.H. (2006).
    Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.
    BMC Bioinformatics, 7:173.
14. Mathews, D.H. (2004).
    Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.
    RNA, 10:1178-1190.
15. Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H. (2004).
    Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
    Proc. Natl. Acad. Sci. USA, 101:7287-7292.
16. Ding, Y. and Lawrence, C.E. (2003).
    A statistical sampling algorithm for RNA secondary structure prediction.
    Nucleic Acids Res., 31:7280-7301.
17. Matveeva, O.V., Mathews, D.H., Tsodikov, A.D., Shabalina, S.A., Gesteland, R.F., Atkins, J.F. and Freier, S.M. (2003).
    Thermodynamic criteria for high hit rate antisense oligonucleotide design.
    Nucleic Acids Res., 31:4989-4994.
18. Mathews, D.H. and Turner, D.H. (2002).
    Dynalign: An algorithm for finding the secondary structure common to two RNA sequences.
    J. Mol. Biol., 317:191-203.
19. Mathews, D.H., Burkard, M.E., Freier, S.M., Wyatt, J.R. and Turner, D.H. (1999).
    Predicting oligonucleotide affinity to nucleic acid targets.
    RNA, 5:1458-1469.
20. Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H. (1999).
    Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure.
    J. Mol. Biol., 288:911-940.
21. Wuchty, S., Fontana, W., Hofacker, I.L. and Schuster, P. (1999).
    Complete suboptimal folding of RNA and the stability of secondary structures.
    Biopolymers, 49:145-165.