This lecture presents diverse methods that have been suggested for RNA secondary structure comparison. This field has been a very active one recently, where numerous new methods of increasing sophistication have been presented. However, the lecture will argue that we already have adequate methods for different purposes, and further research should concentrate on refining these.

We cover base pair metrics, mountain metrics and different tree metrics, focussing on the problem of structure representation and potential artefacts introduced by representation. We also draw the connection between tree metrics and base pair metrics of aligned (and hence gapped) structures, and touch on the important special case of measuring structure conservation.