[EMBOSS] use water/matcher to find where RNA bybridizes

[Guy Bottu]

On Thu, Jun 02, 2005 at 07:52:45AM -0700, David Mathog wrote:
> > One of our users had a problem : how to find the location where a small 
> > molecule of RNA binds to a mRNA and so interferes with its functioning. 
> 
> This can also be addressed with Mfold.  Let A be the large mRNA of
> length N and B the small one of length M. Create a hybrid RNA sequence
> AB of length N+M.  Set the rules in mfold so that
> 
>   bases 1->N will not bind with bases 1->N
>   bases N+1->N+M will not bind with bases N+1->N+M

Clever idea ! As a matter of fact, I had thought of doing that, with the 
extra of putting between both a linker of 200 T's wich are not allowed to 
pait at all. Unfortunately the program mfold crashed with message :

Fill run failed

Maybe there is something unusual in the sequence.

	Regards,
	Guy Bottu,
	BEN