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