[Jalview-discuss] adding features to gaps in a sequence

[James Procter]

Simren Mehta wrote:
> Yet another question. Is it possible to colour in gaps that are at the end of a
> specific sequence in an alignment, to highlight that these residues are missing
> in a given protein? When i tried to do this it added the feature to the last
> residue of the sequence (not to the gaps i selected) and i couldn't figure out
> how to undo it. Is there a way to do this?
Gaps cannot be coloured with a sequence feature. Typically, you would 
use either an 'X' or an 'N' to indicate that a residue or base is 
present but its identity is unknown, and (optionally) define a feature 
on those positions.

If you want to colour gaps then you could define a group over that 
region, and pick its colour (if you do this with an annotation file you 
can also set a single background colour - see the 'colour' property in 
http://www.jalview.org/help/html/features/annotationsFormat.html ).

hope this helps
Jim.