Structure prediction on DNA folding form or RNA folding form

Question

[The Last Word]

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.

[Sean Davis]

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

[Alastair Kerr]

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: http://www.tbi.univie.ac.at/RNA/

Answer 1

[Michael]

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