How To Find Known Local Secondary Structures In Rna

Question

[Nicolas Rosewick]

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.

[Zhidkov]

take a look at these:
1.locarna
2.rfam
3.infernal

[Michael]

This would well qualify as an answer?

[Nicolas Rosewick]

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.

[Andreas]

Would RNA(p)lfold work for you?

Answer 1

[marco23.p]

Hi! In my lab I am currently working on a motif finder for RNA secondary structures (no needing for previous alignments). Just wait a bit and it will be released ; )