| ## RNAstructure Installation and Overview Software Package Components | ### Contents ### Index
## Single Sequence Methods
Feature | Text Interface Program | JAVA 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
Predict canonical and non-canonical pairs. | CycleFold | N/A | N/A
Design a sequence to fold with low ensemble defect to a target structure. (Reference: Bellaousov et al. 2018) | design | N/A | Design
Drawing secondary structure diagrams | draw | Draw | RNA::DetermineDrawingCoordinates
Ensemble defect calculator. (Reference: Bellaousov et al. 2018) | EDcalculator | N/A | N/A
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
Use a genetic algorithm to select a sequence that avoids base pairs | orega | N/A | N/A
Estimate base pairing probabilities and probabilities of structures. 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
Calculation of loop probabilities (Reference: Sloma and Mathews 2016) | ProbScan | N/A | ProbScan
Remove Pseudoknots (Reference: Smit et al. 2008) | RemovePseudoknots | Break Pseudoknots | RNA::BreakPseudoknot
Predict multiple folding conformations, guided by SHAPE data. (Reference: Spasic et al. 2018) | Rsample | N/A | Rsample
Caculate the per nucleotide Shannon entropy in a sequence | Shannon | N/A | N/A
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 GUI Menu Item | Class Library and Function Name
--- | --- | --- | ---
Predict bimolecular base pairs while accounting for preexisting structure.DiChiacchio et al 2016. | AccessFold | N/A | HybridRNA::AccessFold
Predict a common structure for a set of aligned sequences. | AlignmentFold | N/A | RNA:FoldSingleStrand (after reading a sequence alignment in RNA constructor.)
Predict base pairing probabilities for common structure for a set of aligned sequences. | AlignmentPartition | N/A | RNA:PartitionFunction (after reading a sequence alignment in RNA constructor.)
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
Predict conserved pairs, both canonical and non-canonical. | CycleFold | N/A | N/A
Bimolecular structure prediction without intramolecular pairs | DuplexFold | N/A | HybridRNA::FoldDuplex
Predict a secondary structure common to two homologs. Dynalign (References: Harmanci et al. 2007, Uzilov et al 2006, Mathews and Turner 2002) | dynalign | RNA Dynalign | Dynalign_object::Dynalign
Predict a secondary structure common to two homologs, allowing structure domain inserts. Dynalign II | dynalign_ii | N/A | Dynalign_object::Dynalign (Built by defining DYNALIGN_II at precompile time)
Predict if a set of input sequences have a conserved secondary structure | Multifind | N/A | N/A
Predict a common secondary structure to multiple homologs. Multilign (Reference: Xu and Mathews, 2011) | multilign | RNA Multilign | Multilign_object::ProgressiveMultilign
Assess the duplex formation thermodynamics for a set of oligonucleotides. OligoScreen Reference: Mateeva et al. 2003) | oligoscreen | OligoScreen | Oligowalk_object::OligoScreen
Find high affinity oligonucleotides to a structured RNA target. 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
Predict the common secondary structure and multiple sequence alignment for multiple sequence homologs. TurboFold References: Harmanci et al. 2011, Tan et al. 2017) | TurboFold | RNA TurboFold | TurboFold::fold
Predict a secondary structure by homology modeling when the structure and alignment is available for sequence homologs. TurboHomology | TurboHomology | N/A | TurboHomology
## Utilities
Feature | Text Interface Program | JAVA 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
Identify sequences that are are not homologous to others in a set | DecoyFinder | N/A | N/A
Cluster structures in a CT file | Diana_Cluster.R | 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
Graphical Secondary Structure Editing and Drawing | Standalone Program: StructureEditor
Test the required symmetries in a set of thermodynamic parameters | SymmetryTester | N/A | N/A
Free energy calculation library | C++ Source Code (class library) RNAstructure/efn_lib Written by Max Ward (PhD Candidate, University of Western Australia)
### References Bellaousov, S., Kayedkhordeh, M., Peterson, R. J. & Mathews, D. H. (2018). Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops. RNA. 24: 1555-1567. Spasic, A., Assmann, S. M., Bevilacqua, P. C., & Mathews, D. H. (2018). Modeling RNA Secondary Structure Folding Ensembles Using SHAPE Mapping Data. Nucleic Acids Research. 46: 314-323. Tan, Z., Fu, Y., Sharma, G., & Mathews, D. H. (2017). TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. Nucleic Acids Research. 45: 11570-11581. Sloma, M.F., & Mathews, D.H. (2016). Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures. RNA. 22: 1808-1818. DiChiacchio, L., Sloma, M. F., & Mathews, D. H. (2016). AccessFold: Predicting RNA-RNA Interactions with Consideration for Competing Self-Structure. Bioinformatics. 32: 1033-1039. 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. Xu, Z., and Mathews, D.H. (2011). Multilign: An algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinformatics, 27:626-632. Bellaousov, S., and Mathews, D. H. (2010. ProbKnot: fast prediction of RNA secondary structure including pseudoknots. RNA. 16:1870-1880 Harmanci, A.O., Sharma, G. and Mathews, D.H. (2009). Stochastic sampling of the RNA structural alignment space. Nucleic Acids Res., 37:4063-4075. 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. 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. 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. 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. 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. 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. Lu, Z.J. and Mathews, D.H. (2007). Efficient siRNA Selection Using Hybridization Thermodynamics. Nucleic Acids Res., 36:640-647. 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. 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. 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. 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. Ding, Y. and Lawrence, C.E. (2003). A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31:7280-7301. 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. 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. 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. 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. 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.