Question: How To Find Known Local Secondary Structures In Rna
2
gravatar for Nicolas Rosewick
7.0 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k wrote:

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.

rna structure • 2.8k views
ADD COMMENTlink modified 5.4 years ago by marco23.p20 • written 7.0 years ago by Nicolas Rosewick9.0k
2

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

ADD REPLYlink modified 7.0 years ago • written 7.0 years ago by Zhidkov570

This would well qualify as an answer?

ADD REPLYlink written 7.0 years ago by Michael Dondrup47k

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.

ADD REPLYlink written 7.0 years ago by Nicolas Rosewick9.0k

Would RNA(p)lfold work for you?

ADD REPLYlink written 7.0 years ago by Andreas2.5k
0
gravatar for marco23.p
5.4 years ago by
marco23.p20
European Union
marco23.p20 wrote:

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 ; )

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by marco23.p20
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