[Biopython] RNA Secondary structure

[Gregory Barendt]

Does anyone know of good libraries for looking at RNA secondary structure? I'm looking for particular stem loops in particular locations in lots (hundreds of thousands) of sequences. 

Right now, I'm pretty inelegantly parsing the .ct file generated by UNAfold. I need to modify my search to be a little more flexible, so I'd much rather use an existing tool than continue to reinvent the wheel. Any advice would be greatly appreciated.

Thanks,
Greg