Entering edit mode
9.8 years ago
Nicolas Rosewick 10k
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 :
- To check for known structure in databases ( which databases ?)
- 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.
take a look at these:
This would well qualify as an answer?
Thanks. But I don't have multiple alignment of my sequences. Each sequence is different (and very long : > 10kb) and I want to check for over-represented local structure.
Would RNA(p)lfold work for you?