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

[pmr at ebi.ac.uk]

Dear Guy,

> 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.

I believe it is perturbed by the zero score for identical base pairs. This
makes it unable to find a consensus character for the alignment, and so
the "no consensus found" '.' character appears in the output.

Making the output format understand your non-identical matching is an
interesting challenge. I will look into it a little more.

regards,

Peter