Hi,

I would like to compare a set of RNA molecules that share the same core or actually make a map of similarity between them (structurally around 50% residues are conserved).

What do you think what metric and a way of aligning them I should use?

Is there better way than:

The key component of any structural database is the 3D structural alignment. A number of research groups developed programs for RNA structural alignment including DIAL (14), SARA (15), SARSA (16), iPARTS (17), ARTS (18), LaJolla (19) or R3D Align (20). The common limitations of these approaches include the restriction on the size of aligned structures or the low speed when aligning large RNA molecules. In this article, we introduce a SETTER web server utilizing our novel SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm (21) for RNA structure pairwise comparison. The most relevant feature of the method is that it performs at significant speeds even for largest RNA structures (no size limit is imposed on aligned structures) without compromising accuracy of the alignment.

http://nar.oxfordjournals.org/content/early/2012/06/11/nar.gks560.full

Magnus