{Enter a description of your molecule and the known base-pairing into your notebook.}

{B. MFOLD - multiple sub-optimal RNA structures.}

{1. Learn about the GCG programs MFOLD in GENHELP.}

{2. Use PLOTFOLD to examine the squiggles, mountains, circles, domes, and dotplot output from MFOLD.}

{3. Use PLOTFOLD to examine at least five of the sub-optimal folds produced by MFOLD. What graphics output is most useful in this comparison?  Which one of these structures, if any, corresponds to the known structure of your RNA? }

{C. MFOLD parameters: constraining the folding pattern.}

{1. Based on your knowledge of the biology of your molecule (and/or the annotation in the sequence file), use some of the parameters of MFOLD: /REMOVE /PREVENT /FORCE.}

{D. Using the GCG programs STEMLOOP and DOTPLOT for RNA structures.}

{1. Learn about the GCG STEMLOOP program using GENHELP.  Analyse your sequence using STEMLOOP and display your results using DOTPLOT.}

{2. Compare these results with those from MFOLD as displayed using PLOTFOLD.}

{3. Attempt to find a set of parameters for STEMLOOP which yields output in which you can see the stems predicted using MFOLD.}

{E. Questions.}

1. What are the problems with the SQUIGGLES representation for RNA structures?
2. Name a representation that corrects these problems?
3. What is the difference between an internal loop and a bulge loop?
4. What are the advantages of MFOLD relative to STEMLOOP?
5. What are the disadvantages of MFOLD relative to STEMLOOP?
6. What kinds of structures cannot be found by folding programs such as MFOLD?
7. In general, which will destabilize a structure more: an internal loop or a bulge loop. Explain your
8. answer and include energies.
9. What are the main energy terms considered in computer prediction of RNA folding?
10. List the favorable energy terms (those that stabilize structures) in RNA folding?
11. When is a GU basepair less stable that of a AU basepair?
12. What laboratory methods might one use to test the correctness of a predicted structure?
13. What non-laboratory (e.g., computational) methods might on use to test the correctness of a predicted structure?
14. What is a P-num plot and why would one use it?