Question about Mulfold (M. Zuker et al.'s)

Erik Forbes Y. Hom '95 ehom1 at cc.swarthmore.edu
Wed Dec 7 09:35:33 EST 1994

Hi netters!  I have a copy of mulfold for the Mac.  A limitation of this
version: one can only fold a 300 base sequence.  I, however, have a
sequence of ~4000 that I want to fold to see if the start codon or SD
domain could potentially interact with bases more distant than the
neighboring ~150 bases (and the effect of mutations in these more distant
domains on this interaction).  Is there anyway I could do this without
constructing some chimeric sequence between the initiation region and the
distant region of interest (I don't think the results I would get from this
would be very realistic)?  Do you thing it is reasonable
(thermodynamically) for a such a distant region (say ~500 bases away) to
base pair with the initiation region?  (I can't, for certain, justify one
or the other because I can't do the folding!).  What are the limitations
for the UNIX version??  Help!  Thanks for your time!

Yours truly,


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