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

Jasper Rees - tel +44 865 275567 jasper at molbiol.ox.ac.uk
Mon Jun 27 07:57:24 EST 1994

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.uk
system at molbiol.ox.ac.uk

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