| ## RNAstructure GUI Help References | ### Contents ### Index
Research benefitting from RNAstructure should cite: J.S. Reuter and D.H. Mathews. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010). The algorithms central to RNAstructure are based on the following sources. Research benefitting from these capabilities encapsulated within RNAstructure should cite the appropriate sources. Most current folding parameters: D.H. Mathews, M.D. Disney, J.L. Childs, S.J. Schroeder, M. Zuker, and D.H. Turner. "Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure." Proceedings of the National Academy of Sciences USA, 101:7287-7292. (2004). Previous reference to the folding algorithm, with details on thermodynamic parameter derivation: D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner. "Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure." Journal of Molecular Biology, 288:911-940. (1999). Prediction of secondary structures at temperatures other than 37°C: Z.J. Lu, D.H. Turner, and D.H. Mathews. "A Set of Nearest Neighbor Parameters for Predicting the Enthalpy Change of RNA Secondary Structure Formation." Nucleic Acids Research, 34(17):4912-24. (2006). Partition function for calculating base pair probabilities: D.H. Mathews. "Using an RNA Secondary Structure Partition Function to Determine Confidence in Base Pairs Predicted by Free Energy Minimization." RNA, 10:1178-1190. (2004). Dynalign: D.H. Mathews. "Predicting a Set of Minimal Free Energy Secondary Structures Common to Two Sequences." Bioinformatics, 21:2246-2253. (2005). Extensive use of Dynalign (for extensive acceleration of the algorithm): A. Harmanci, G. Sharna, and D.H. Mathews. "Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign." BMC Bioinformatics, 8:130-150. (2007). Previous reference to Dynalign: D.H. Mathews and D.H. Turner. "Dynalign: An Algorithm for Finding the Secondary Structure Common to Two RNA Sequences." Journal of Molecular Biology, 317:191-203. (2002). OligoScreen: O.V. Mateeva, D.H. Mathews, A.D. Tsodikov, S.A. Shabalina, R.F. Gesteland, J.F. Atkins, and S.M. Freier. "Thermodynamic Criteria for High Hit Rate Antisense Oligonucleotide Design." Nucleic Acids Research, 31:4989-4994. (2003). OligoWalk: D.H. Mathews, M.E. Burkard, S.M. Freier, J.R. Wyatt, and D.H. Turner. "Predicting Oligonucleotide Affinity to Nucleic Acid Targets." RNA, 5:1458-1469. (1999). DNA/RNA duplex parameters for DNA oligomers: N. Sugimoto, S. Nakano, A. Katoh, H. Nakamura, T. Ohmichi, M. Yoneyama, and M. Sasaki. "Thermodynamic Parameters to Predict the Stability of RNA/DNA Hybrid Duplexes." Biochemistry, 34:11211-11216. (1995). Prediction of all suboptimal secondary structures: S. Dian, D.H. Mathews, and D.H. Turner. "Interpreting Oligonucleotide Microarray Data to Determine RNA Secondary Structure. Application to the 3' End of Bombyx mori R2 DNA." Biochemistry, 45:9819-9832. (2006). Methods for predicting suboptimal secondary structures: D.H. Mathews. "Revolutions in RNA Secondary Structure Prediction." Journal of Molecular Biology, 359:526-532. (2006). Original reference to generating all suboptimal secondary structures for a sequence: S. Wuchty, W. Fontant, I,L. Hofacker, and P. Schuster. "Complete Suboptimal Folding of RNA and the Stability of Secondary Structures." Biopolymers, 49:145-165. (1999). Stochastic sampling: Y. Ding and C.E. Lawrence. "A Statistical Sampling Algorithm for RNA Secondary Structure Prediction." Nucleic Acids Research, 31:7280-7301. (2003). Using SHAPE data to constrain structure prediction: K.E. Deigan, T.W. Li, D.H. Mathews, and K.M. Weeks. "Accurate SHAPE-directed RNA Structure Determination." Proceedings of the National Academy of Sciences USA, 106: 97-102. (2009). Photocleavage of uracil in the presence of FMN: P. Burgstaller, T. Hermann, C. Huber, E. Westhof, and M. Famulok. "Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices." Nucleic Acids Ressearch, 25:4018-4027. (1997). ProbKnot pseudoknot prediction algorithm: S. Bellaousov and D. H. Mathews. "ProbKnot: fast prediction of RNA secondary structure including pseudoknots." RNA, 16:1870-1880. (2010). Multilign: Z. Xu and D. H. Mathews. "Multilign: An algorithm to predict secondary structures conserved in multiple RNA sequences." Bioinformatics, 27:626-632. (2011) TurboFold: A. O. Harmanci, H. Sharma,and D. H. Mathews "TurboFold: Iterative Probabilistic Estimation of Secondary Structures for Multiple RNA Sequences." BMC Bioinformatics, 12:108. (2011).