RNA secondary structure comparison
You can use R-coffee of the T-coffee suite of tools. In general, the *coffee tools are excellent and work very well if you can get over their author's self obsession1. R-coffee can align RNA sequences taking into account structural information:





1 The guy actually adds his name to the output of all his programs! Seriously, he does. Apart from being simply ridiculous, this also affects other programs you might want to pipe your data to. For example, I wanted to pipe t-coffee alignments to an alignment viewer and I had to parse out his effing name in order to be able to do it.