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RNAstructure Installation and Overview
Software Package Components

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.