I recently had to modify Jalview 2.4 to add a feature that may be useful for a wider audience.
Basically, the idea is to modify the view of the multiple alignment in such a way that only the residues that are not matching the consensus are displayed (to emphasize non conserved regions in a highly conserved alignment). Other residues can be replaced by any relevant/neutral character. Users can switch from one view to the other by selecting a menu entry. I've got some code I can share if you're interested.
I recently had to modify Jalview 2.4 to add a feature that may be useful
for a wider audience.
great!
Basically, the idea is to modify the view of the multiple alignment in
such a way that only the residues that are not matching the consensus
are displayed (to emphasize non conserved regions in a highly conserved
alignment). Other residues can be replaced by any relevant/neutral
character. Users can switch from one view to the other by selecting a
menu entry. I've got some code I can share if you're interested.
It sounds like this provides a very useful view (in fact, a couple of
people have asked for this).
My own plans for implementing a view like was to create a new kind of
alignment colourscheme. Each group defined on the alignment has its own
consensus sequence, which a colourscheme implementation has access to,
so all that was required was to enable the colourscheme interface to
modify the residue symbol in addition to the residue background colour).
But, sadly, I haven't gotten around to this as yet.
I would be interested to see how you have implemented it and if there
are no conflicts caused by the strategy you've taken, I'll try to
incorporate into the jalview source...
thanks!
Jim.
···
--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.