adding features to gaps in a sequence

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?

Thanks for all your help.

Simren

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.