How To Find Known Local Secondary Structures In Rna
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10.9 years ago

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 • 3.9k views
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2
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take a look at these:
1.locarna
2.rfam
3.infernal

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This would well qualify as an answer?

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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.

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Would RNA(p)lfold work for you?

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9.3 years ago
marco23.p ▴ 20

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 ; )

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