High throughput RNA secondary structure predictor

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7.8 years ago

blur ▴ 280

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 • 1.8k views

ADD COMMENT • link 7.8 years ago by blur ▴ 280

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

ADD REPLY • link 7.8 years ago by Michael 55k

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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

ADD REPLY • link 7.8 years ago by blur ▴ 280

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You can install it locally and run all sequences in batch

ADD REPLY • link 7.8 years ago by Asaf 10k

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

ADD REPLY • link 7.8 years ago by blur ▴ 280

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

ADD REPLY • link 7.8 years ago by blur ▴ 280

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RNAfold of Vienna package, mfold etc.

ADD REPLY • link 7.8 years ago by Asaf 10k

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