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

[David Mathog]

> 
> 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

Run Mfold.
Look through the results.

If this runs properly you should see B bound somewhere in A with
an energy level you may then use to compare binding affinities. 

Regards,  

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech