Fundamentals of Sequence Analysis, 1998-1999
Problem set 9:  RNA folding.

If you get stuck, refer to the OpenVMS and GCG resources in the 
class home page.

  See the GCG documentation.

Problem group 1.  Stem-loop structures

1A.  Are there any stem/loop structures in the tet gene of pBR322 that
     have at least 16 hydrogen bonds in the stem?

Problem group 2.  RNA folding

2A.  Does the tet RNA from pBR322 have a defined secondary structure?

2B.  Does the 3' end of the Drosophila bicoid mRNA have a defined
     structure?  (gb_in:X14458, 1550-2456)

Problem group 3.  RNA folding with pseudoknots
It is a good idea to rerun MFold and PlotFold for
sequences which may include pseudoknots.  However, doing so is
actually a little tricky.  The problem is that if you try to force
MFold to have pseudoknots, it will ignore one of the two
helices specified, unfortunately, without giving any warning that it
is doing so.  If you try to exclude these regions with /Closedexcise,
MFold will ignore that directive in some instances.  This is a
bug of some sort.  This leaves only the /prevent qualifier,
which may be used to force the pseudoknot regions into a large,
noninteracting loops. 

3A.  Use RNABOB to analyze gendocdata:alucons.seq, then run
     MFold and PlotFold to see how removing the
     pseudoknot regions affects the rest of the fold. 

3B.  Use PlotFold to output a connect file, manually edit
     it so that the pseudoknot links are present, then use 
     Squiggles to display it.  What happens?