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I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but these only allow from prediction of secondary structure of the ribozyme folding on itself (which is thermodynamically less stable that 20-40 perfectly complementary nucleotides along the arms).

Is there any software that will allow for simultaneous prediction of secondary structure of two RNA molecules?

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there is a software called UNAfold (same website as mFold) which allows nucleic acid hybridization. –  WYSIWYG Aug 17 '13 at 4:07
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