RNA SECONDARY STRUCTURE

westerm at aclcb.purdue.edu westerm at aclcb.purdue.edu
Thu Jan 13 13:36:45 EST 1994


In article <2gt1ei$94e at athena.cs.uga.edu> ramanath at pollux (CHANDRA RAMANATHAN) writes:
>   Most of the programs handle only small RNA sequences.  Is there any program
>   which can handle big sequences(10,000 bp).  I have some access to 
>   supercomputing facilities, which these big sequences require.  I would 
>   highly appreciate if you can help me in this regard.

The existing programs don't predict correct structures for small
sequences and thus there is no reason to suspect they will predict
larger sequences with any accuracy. All you will get is garbage.
Never-the-less, if you wish to modify the source code for MFold
and you have a large enough computer, you should be able to run 
MFold on 10,000 bases. I've done a "pseudo-fold" (that is, just 
looking at the closest 200 bp when considering a fold instead of
doing a true global folding) on HIV (~10,000 bp) using both MFold 
and a yet-to-be-released custom RNA folding program. It works. It
took days of computer time. And the results were unreliable. But
it can be done.


If you limit MFold to just examining the 



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