How can I correctly predict RNA secondary structure?

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Christopher Bystroff

Try MFOLD (Unafold). (http://unafold.rna.albany.edu/)

You'll find that it gives you more information than you asked for!

It uses an energy-based approach. All basepairings have an energy associated (not just Watson Crick!) and all possible base-pair stackings are also considered. Unafold uses dynamic programming to implicitly consider all possible foldings. Pseudoknots (where bases in a loop can basepair with bases outside the loop) are not allowed in the algorithm because pseudoknots violate the dynamic programming assumptions.

Thoria Donia

Thanks Prof.Christopher I already know the program and can use but I used default conditions as I do not know what the optimal conditions for right folding and about energy association I really can not understand this part well because I always get more than 1 or 2 secondary structure predictions for the specific sequence and they are completely different and I can not guess which one is the most right predicted form. Also, I think this form should be used in another program to predict the tertiary structure I really can not imagine how these working may be more chemistry concepts are involved in these type of predictions

Prof. Artur Burzynski

I think all concepts in science start simple but we make it more complicated to understand what we need so may non-specialists take more time to get to simple again and proceed gradually

Thoria, if you get more than one answer then the program is predicting that there will be more than one conformation present in solution. Multiple answers does not mean the outcome is uncertain but that there are multiple right answers. You should use the conditions that match the expected experimental conditions. There is no "optimal".