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

[Fernan Aguero]

+----[ Guy Bottu <gbottu at ben.vub.ac.be> (02.Jun.2005 07:13):
|
| mRNA            2892 AATGTTGTGTGAGGATAATAGTAATAGTAATAGTAATAATAATAATAAT  2940
|                      ..  . . .... ... .. .. .. .. ..  ................
| RNAi               1 TTTGACCCTGCTACTACTACTACTACTACTACGATTATTATTATTATTA  49
| --------------------------------
| The only thing which bothers me is that the base pairs (which do have a 
| positive comparison score) are not labeled as "similar", they get a '.' 
| instead of a ':'. Does someone know why this is ?
|
+----]

Guy,

just a guess, but '.' and ':' are used in protein-protein
comparisons to denote identity and similarity which are both different
and meaningful. In dna-dna comparisons, you only care for
identity, whether you consider it to be aligning A with A or
A with its complement. So I would only expect only one of
'.' or ':' used ... don't remember which is used for
identity in emboss.

My 2 cents guess,

Fernan