title: Predicting the secondary structure common to two RNA sequences with Dynalign.
abstract: 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.
authors.affiliation: Center for Human Genetics and Molecular Pediatric Disease Aab Institute of Biomedical Sciences University of Rochester Medical Center, Rochester, New York, USA.
authors.forename: David
authors.initials: D
authors.lastname: Mathews
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics* / Q000648:ultrastructure*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012313:RNA