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Request: RNA folding prog. w/ ~2.5 kb RNA?

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Sat Jun 25 09:26:15 EST 1994


modifying the source to mfold or other rna folding program is
your main option.  The reason large molecules like 2.5kb are not
normally supported is that it takes a huge chunk of memory
for a program to deal with rna folding that size, and a lot
of cpu time.  Be prepared for a good long wait, depending
on how fast your computer is, for the results.  I think analysis time
is proportional to the cube of the size of the molecule.

Your GCG version of mfold source is likely on your computer
in the gcg/source location.  But if you can't find it, you can
dig up Michael Zuker's original mfold source at this ftp location:

nrcbsa.bio.nrc.ca:
        -Michael Zukers software for folding with multiple suboptimal
         scores, viewing of structures and more.


-- Don
-- 
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu




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