Hi,

I've a bunch of RNA sequence to check for known local secondary structures, and also to check for enriched local secondary structure between them. Is there a tool available ? If not my idea was to cut each sequence in overlapping part, to predict the secondary structure and then :

1. To check for known structure in databases ( which databases ?)
2. cluster together each local structure using RNAdistance and check for over-represented local structure.

I don't want to reinvent the wheel so if there is an available tool I prefer to use it.

Thanks,

N.