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,
erik
