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Newbie with RNA folding troubles

Andres Moreira andres.moreira at terra.cl
Mon Nov 3 07:05:59 EST 2003

Thank you for your hint (here, and in the email). I tried mfold, and it 
gave the same result as the Vienna package. In fact, when I asked for 
suboptimal structures, the second-best was the structure with all 9 
pairs. So, I supposed that the reason is a strain in the loop. But then, 
I don't understand why RNAdraw (which uses the same algorithms) DID join 
that base pair, and instead, failed to join the two bases at the other 
extremity of the stack (where there is no loop). Different energy 
parameters? May it be so sensible to that?

William Knight wrote:
> Lack of a-u base pair on the right is probably because it would cause
> strain in the loop.  Trying folding with mfold and viewing some of the
> resulting secondary structures.
> William Knight
> ---


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