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

[Guy Bottu]

	Dear all,

Thanks for your replies. It is however still not clear to me where the '.' 
come from. I thought the EMBOSS "pair" output would put a '|' for 
identities and a ':' for similarities (score positive). Maybe the program 
is fooled and seriously perturbed by a matrix that assigns a negative 
score to identical base pairs.

As for the proposal to distribute ViennaRNA as an Embassadir, why not ? At 
the BEN site we have mfold integrated under EMBOSS, but I am afraid 
distributing mfold as Embasadir will turn out to be impossible bacause of 
licencing issues.
Note that mfold does not entirely solve the problem, since it operates on 
a single sequence, it does not search for a structure composed of two 
strands. I guess this is also true for ViennaRNA.
We (me and our user) had tried to use mfold (with as input a sequence 
composed of the mRNA, a poly-T linker and the small RNA), but the program 
crashed with error message "Cannot get Fill". Maybe the sequence had 
something unusual.

	Regards,
	Guy Bottu,
	BEN