Dear Jalview Discussion Group,
I have been using the alpha helix and beta sheets annotation function in Jalview to label a genome alignment with protein names at the bottom of the MSA. Is there a way to modify the colors and of these annotations? Ideally, I’d use the alpha helix shape since it doesn’t have the beta sheet arrow. Is this a possibility? Or is there another way to accomplish the task? Any help you may provide is appreciated.
Thanks,
Heather Driscoll
Dear Heather, thanks for posting !
I have been using the alpha helix and beta sheets annotation function in Jalview to label a genome alignment with protein names at the bottom of the MSA. Is there a way to modify the colors and of these annotations?
Unfortunately not currently, but you've raised a good case for doing it. We'll hopefully be adding new annotation row functionality for release in early 2021.. we'll try and fit this in ! (you can sign up on our bug tracker and hit the 'Watch' button to get updates on the issue here https://issues.jalview.org/browse/JAL-3752).
Ideally, I'd use the alpha helix shape since it doesn't have the beta sheet arrow. Is this a possibility? Or is there another way to accomplish the task? Any help you may provide is appreciated.
Right now, the only thing I can suggest is a workaround. You can use a jalview annotation file to add an additional 'BAR_GRAPH' annotation row which is all '0' except where genes occur (add a 1 instead). You can then also specify each bar's colour to achieve the effect you want, albeit in a clumsy fashion.
I'm sure you've seen it, but the documentation for creating Jalview annotation files is here:
http://www.jalview.org/help/html/features/annotationsFormat.html#annrows
Jim.
PS. You can configure the symbol shown below each histogram as well, so you don't actually see the values creating the bar!
On 16/09/2020 22:04, Heather E. Driscoll wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk