Comparing RNA structures

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jkominek
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Joined: 04/28/2014

Hi, I've recently been trying to identify the effects that certain point mutations have on the mRNA of my genes of interest. To do that, I am using several RNA secondary structure prediction tools (including mfold) and using whatever comparison tools are implemented to see if the difference in structure is big or small (e.g. 'ct_compare' in mfold). I would like to ask about what's the best way to do it? Right now, for simplicity, I'm looking only at the MFE structures, compare their energies and structures. Should I be looking maybe at the entire ensembles and comparing them somehow? If so, how? Any advice would be appreciated :)