Question: Structure prediction on DNA folding form or RNA folding form
gravatar for The Last Word
5.6 years ago by
The Last Word200
The Last Word200 wrote:

I don't know how stupid of a question this is so please bear with me. I have a certain number of EST cDNA sequences that I used for miRNA prediction. The results are cDNA sequences so for the secondary structure prediction of precursor miRNA, should I use the RNA folding form or the DNA folding form on Mfold because it gives both options and I am confused on which should I use. DNA folding because my sequences are cDNA sequences or RNA folding form because I am trying to predict pre-miRNA sequences after all. Please advice.

mirna mfold • 2.4k views
ADD COMMENTlink modified 5.6 years ago by Michael Dondrup48k • written 5.6 years ago by The Last Word200

It seems like converting to RNA first and using the RNA folding would make the most sense?  

ADD REPLYlink written 5.6 years ago by Sean Davis26k

As others have mentioned, you should be looking at RNA.  You may also want to look at a more recent folding predictor such as the latest Vienna RNA:

ADD REPLYlink written 5.6 years ago by Alastair Kerr5.3k
gravatar for Michael Dondrup
5.6 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

I think you should use RNA parameters because miRNAs are indeed RNA, that doesn't depend on how the sequence was acquired.

ADD COMMENTlink written 5.6 years ago by Michael Dondrup48k
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