Predicting the Secondary Structure Common to Two RNA Sequences with Dynalign

This is the authors' abstract. We don't add key points for this paper.

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.