Dear all, I’ve been looking for the following feature for a long time, either in Jalview or other software. Is there any mean to add “text” annotations to a specific residue in a alignment, in a way that is reasonably easy to display ?
The use case is for instance to annotate within an alignment which specific residues have been targeted by site-directed mutagenesis, in which paper, which were the results, and so on… This would be tremendously useful for planning mutagenesis campaigns.
I tried to abuse the annotation system for this, but I only managed to change color of residues, but not add displayable text. Is there a way to do that now ? If not, would you be interested if I try to write that ?
These kinds of information are definitely best stored as sequence features rather than annotation tracks. However, as you say, there is no convenient way of visualising all the information in a feature beyond the feature shading system (which is incredibly flexible, but never the less is only designed to encode feature data as colours).
We would be very pleased if you’d consider developing something ! Perhaps the first thing is to create a visual mock up of what you want ? That way, I can suggest the shortest path to implementing it
Thanks for the quick answer. What I’m thinking about for now is probably just a specific shading/background/small icon and a mouseover text displaying the free annotation, that would already be extremely useful. I guess starting from this it would probably evolve into something more practical, but not before we get a chance to try it. Is that enough information for you or do you want an image for that ?
OK… I think sequence features already does what you need. For instance, the specific shading + tooltip is already available, with the context menu allowing access to details for a particular feature shown as a popup window:
There’s currently no additional encoding such as display of an icon, however. That certainly could be easily implemented. The hardest part there is deciding on what icon is shown, and how to extend the feature style GUI (https://www.jalview.org/help/html/features/featureschemes.html) and how the setting is represented in Jalview’s feature file format!
Probably the main issue is how you plan to get these data into Jalview. The interactive feature creation dialog just allows you to define the colour and enter text or html, but doesn’t allow additional attributes to be created - only VCF, GFF3 and some database retrieval services currently create additional attributes.
My suggestion is to start with a GFF3 file with all the data you want encoded as positional features with attributes ( https://www.jalview.org/help/html/features/featuresFormat.html#gff ), and then work out what else is needed.
Wow, thanks a lot, I wasn’t aware this was already possible. I’ll dig into that and see how I can generate the GFF3 data that suit my needs, and I’ll tell you my opinions here.
… oh, yes, this is exactly what I need for now ! I just need to setup my internal data to generate the correct output.