RNA Secondary Structure Prediction : what's relevant?

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Tue Dec 2 01:14:54 EST 1997

In article <3475044F.3755 at bccancer.bc.ca>, Paul Kowalski <pkowalsk at bccancer.bc.ca> writes:
>Hi - 
>I've been using GCG's MFold/Plotfold programs to look at possible
>secondary RNA structure (stemloops etc.) which might be found in the 5'
>UTR of the gene I'm working on. The output (I use "squiggle plot") gives
>you a nice picture of optimal and suboptimal structures ranked by the
>minimum energies. 

You probably want to first have a pass through this using menu=b in
plotfold, that is, the P-Num plot.  It shows the number of *different* bases
that each base pairs with in all foldings down to a given energy level
(which, unless you change it, the program sets by default.)  These plots
are a much better tool for finding "real" RNA structures than are
squiggle plots, since when real structure is present the same bases tend to
pair up the same way in the part that is really doing something, resulting
in dips in the P-Num plot.  This can be pretty hard to see in the other 
sorts of plots, but sticks out like a sore thumb in a P-Num plot.  For
instance, see: 


for P-num plots for pBR322 and bicoid.  The former is assumed to have no
RNA structures, and no low P-Num locations are found. The latter is known 
to have RNA structure, and several low P-Num locations show up clearly.


David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 

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