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3. Michael Zuker's mfold (multiple foldings of RNA) is used to find the minimum energy structure of an RNA molecule. Please check with the instructor before going to the RNA analysis page at Use of this Web site must be spread out because the analysis is very computer intensive.
  1. Copy and paste the potato spindle tuber viroid sequence (GenBank accession no. AY360446) into the input window of mfold.
  2. Using the program parameters provided, the immediate option, click the fold RNA box, and wait for the results.
  3. In the output, click on structures 1, 2, 3, etc. to view the alternative structures.
  4. Describe the first structure reported and the energy of this structure.


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