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High throughput RNA secondary structure predictor

Hi,

Can someone recommend a good tool for high throughput tool for RNA secondary structure predictions? I have a few thousand sites that I want to try and detect secondary structures for, but all the papers I've seen include the prior to sequencing the RNA be in some way manipulated. Is there a tool for de novo predictions?

Thanks!

rna-seq rna secondary strucrure
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written by blur blur

Have you tried RNAfold? A local install should be able to handle this size of problems.

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written by Michael Dondrup Michael Dondrup

I tried the server, and it looks like it only takes a sequence at a time... or am I missing something? each one of my sites is a 100bp

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written by blur blur

You can install it locally and run all sequences in batch

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written by Asaf Asaf

thanks, I finally figured it out RNAfold < file Thank you!

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written by blur blur

oh, sorry, I missed the part where you said 'local installer' - thanks!

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written by blur blur

RNAfold of Vienna package, mfold etc.

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written by Asaf Asaf

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