Structure prediction on DNA folding form or RNA folding form
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.
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The Last Word
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I think you should use RNA parameters because miRNAs are indeed RNA, that doesn't depend on how the sequence was acquired.
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Michael Dondrup
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It seems like converting to RNA first and using the RNA folding would make the most sense?
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/