Predicting the Secondary Structure Common to Two RNA Sequences with Dynalign
Dynalign is a dynamic programming algorithm for the simultaneous prediction of the lowest‐free‐energy secondary structure common to two RNA sequences and the alignment of the two sequences. It has been shown that the average accuracy of secondary structure prediction is improved using Dynalign, as compared to free‐energy minimization of a single sequence. This unit provides protocols for using Dynalign on a Microsoft Windows platform as part of the RNAstructure package, and for compiling and using Dynalign on Unix/Linux computers.
Figure 12.4.2 The RNAstructure sequence editor.
Figure 12.4.3 The Dynalign window in RNAstructure. Two tRNA sequences that are included with RNAstructure are selected and the default parameters are shown. The calculation is started by clicking the START button.
Figure 12.4.4 Sample output from the Dynalign algorithm. This is the secondary structure predicted for the tRNA sequence RA7680.
Figure 12.4.5 Dynalign input. User‐provided responses are shown in bold for clarity. This input will predict the common secondary structure and alignment for the two tRNA sequences, RA7680 and RD0260.
|Bruccoleri, R.E. and Heinrich, H. 1988. An improved algorithm for nucleic acid secondary structure display. Comput. Appl. Biosci. 4:167‐173.|
|Burgstaller, P. and Famulok, M. 1997. Flavin‐dependent photocleavage of RNA at G U base pairs. J. Am. Chem. Soc. 119:1137‐1138.|
|Chen, J., Le, S., and Maizel, J.V. 2000. Prediction of common secondary structures of RNAs: A genetic algorithm approach. Nucleic Acids Res. 28:991‐999.|
|Corpet, F. and Michot, B. 1994. RNAlign program: Alignment of RNA sequences using both primary and secondary structures. Comput. Appl. Biosci. 10:389‐399.|
|Eddy, S.R. and Durbin, R. 1994. RNA sequence analysis using covariance models. Nucleic Acids Res. 22:2079‐2088.|
|Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J., and Ehresmann, B. 1987. Probing the structure of RNAs in solution. Nucleic Acids Res. 15:9109‐9128.|
|Gorodkin, J., Heyer, L.J., and Stormo, G.D. 1997. Finding the most significant common sequence and structure in a set of RNA sequences. Nucleic Acids Res. 25:3724‐3732.|
|Hofacker, I.L., Fekete, M., and Stadler, P.F. 2002. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319:1059‐1066.|
|Holmes, I. and Rubin, G.M. 2002. Pairwise RNA structure comparison using stochastic context‐free grammars. In Proceedings of the 7th Pacific Symposium on Biocomputing (PSB 2002), Lihue, Hawaii, January 3‐7, 2002 pp. 163‐174. World Scientific Press, Singapore.|
|Juan, V. and Wilson, C. 1999. RNA secondary structure prediction based on free energy and phylogenetic analysis. J. Mol. Biol. 289:935‐947.|
|Knapp, G. 1989. Enzymatic approaches to probing RNA secondary and tertiary structure. Methods Enzymol. 180:192‐212.|
|Knudsen, B. and Hein, J.J. 1999. Using stochastic context free grammars and molecular evolution to predict RNA secondary structure. Bioinformatics 15:446‐454.|
|Lück, R., Gräf, S., and Steger, G. 1999. ConStruct: A tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Res. 27:4208‐4217.|
|Mathews, D.H. and Turner, D.H. 2002a. Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol. 317:191‐203.|
|Mathews, D.H. and Turner, D.H. 2002b. Use of chemical modification to elucidate RNA folding pathways. In Current Protocols in Nucleic Acid Chemistry (S.L. Beaucage, D.E. Bergstrum, G.D. Glick, and R.A. Jones, eds.) pp. 11.9.1‐11.9.4. John Wiley & Sons, Hoboken, N.J.|
|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.|
|Mathews, D.H., Turner, D.H., and Zuker, M. 2000. RNA secondary structure prediction. In Current Protocols in Nucleic Acid Chemistry (S.L. Beaucage, D.E. Bergstrum, G.D. Glick, and R.A. Jones, eds.) pp. 11.2.1‐11.2.10. John Wiley & Sons, Hoboken, N.J.|
|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. U.S.A. 101:7287‐7292.|
|Pace, N.R., Thomas, B.C., and Woese, C.R. 1999. Probing RNA structure, function, and history by comparative analysis. In The RNA World, 2nd ed. (R.F. Gesteland, T.R. Cech, and J.F. Atkins, eds.) pp. 113‐141. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.|
|Sankoff, D. 1985. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math. 45:810‐825.|
|Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26:148‐153.|
|Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673‐4680.|
|Xia, T., SantaLucia, J. Jr., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., and Turner, D.H. 1998. Parameters for an expanded nearest‐neighbor model for formation of RNA duplexes with Watson‐Crick pairs. Biochemistry 37:14719‐14735.|
|Mathews and Turner, 2002. See above.|
|Describes the Dynalign algorithm and benchmarks the accuracy of secondary structure prediction using Dynalign.|
|Sankoff, 1985. See above.|
|The paper that first proposed using dynamic programming to find a structure common to multiple sequences.|
|The Dynalign algorithm for Microsoft Windows, as part of RNAstructure, is available for download at this URL.|
|The Dynalign algorithm for Unix/Linux is available for download.|