RNA Secondary Structure Prediction : what's relevant?

Paul Edward Kowalski kowalski at unixg.ubc.ca
Mon Nov 24 18:30:55 EST 1997

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. My question is- if the minimum energy value is
dependent upon the the LENGTH of the input sequence, what min. energy
value is significant or relevant? Kozak, J Mol Bio 1994, mentions that
stemloops with a energy of greater than -30 kcal/mol are an impediment
to the scanning 43 ribosome, but the kcal/mol value just depends on how
much seq you give MFold. Is the only way to tell what's relevant to:

A) shuffle the seq of interest -randomize- but maintain the base
composition ratios, and do it again and see if the min energy has


B) Use other "length-matched" DNA sequences from randomly chosen Genbank
entries, and see how their min. energies differ from the test one?

I'm quite confused as to what's important. Any help would be really
appreciated! Email or post. Thanks in advance.

Paul Kowalski
Terry Fox Laboratory, BC Cancer Agency
Medical Genetics, UBC

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