Dynalign is a computer algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity.
Note that Dynalign is now fully incorporated into the RNAstructure package, which is available here.
Mathews, D.H. and Turner, D.H., "Dynalign: An Algorithm for Finding the Secondary Structure Common to Two RNA Sequences," Journal of Molecular Biology 317:191 (2002).
Mathews, D.H. "Predicting a Set of Minimal Free Energy RNA Secondary Structures Common to Two Sequences," Bioinformatics. 21:2246 (2005).Dynalign is also accelerated using the work described in Uzilov, A.V., Keegan, J.M., and Mathews, D.H., "Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change," BMC Bioinformatics. 7:173 (2006) and Harmanci, A., Sharma, G., and Mathews, D.H., "Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign," BMC Bioinformatics. 8:130 (2007).
A record of changes (before integraton with RNAstructure) to Dynalign can be found here .