In article <CryIrr.CCK at usenet.ucs.indiana.edu>, gilbertd at sunflower.bio.indiana.edu (Don Gilbert) writes:
> 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.
Also beware of the diskspace requirements for doing this:
length (bp) size (512 byte blocks under VMS)
100 132
300 1071
500 2964
1000 11757
That makes 2500 bases come out around the 50,000 block (25 MB) range....
I forget the amount of cpu time you would expect this to take, its not
impossible anyway, provided you have enough working set and quotas. You need
to talk to your system manager before you start this I guess...
> Your GCG version of mfold source is likely on your computer
> in the gcg/source location.
Probably worth checking with GCG before you do this, its not a simple as some,
and it sounds like you haven't messed with GCG sources before (no reason not
to start now though :)
regards, jasper
Jasper Rees
Oxford University Molecular Biology Data Centre
and The Sir William Dunn School of Pathology
jasper at molbiol.ox.ac.uksystem at molbiol.ox.ac.uk
