Vienna RNA


How to predict secondary structures of folded RNA:

Download and install Vienna RNA (v1.5beta works on OS X).
In the Terminal, run RNAfold. Paste in your RNA sequence and press Enter, then copy the output sequence and structure data. Press Ctrl-c to end.
Run RNAplot, paste in the output copied from RNAfold and press Enter. A postscript file containing a graphical display of the predicted structure will be saved in the current directory, which can be opened with Preview.
There's probably a way to pipe these commands together, which would be quicker.