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SuLab / WikiGenomesBase

A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.
https://chlambase.org/
MIT License
7 stars 4 forks source link

Ortholog alignment coloring #171

Closed khybiske closed 6 years ago

khybiske commented 6 years ago

@djow2019 This is minor, but is there any way to change the coloring scheme of DNA and amino acid alignments? There are a variety of schemes out there, and everyone has their own preferences... I think the most useful for this module is one where contrast or color was used to highlight divergent bases/amino acids. As opposed to coloring everything. Again, minor...

djow2019 commented 6 years ago

I don't think the MSA viewer supports coloring divergent bases. It uses a static color scheme that gives every base a unique color. I can, however, give you the option to select a colorscheme that you would prefer. I'll re-enable the options bar so we can play around with it.

djow2019 commented 6 years ago

What about something like this image.png

Msa viewer gives the user a menu at the top to dynamically change the color scheme, but for some reason it isn't working (just unresponsive). So we can add the conserved sequences at the top instead.

Check out their example here http://workmen.biojs.net/demo/msa/fer1_annoted and let me know if there is a color scheme that you would prefer. That menu that is shown at the top does not seem to work in chlambase.

Edit: Got the menu bar to work. MSA's major release was bugged. Switched over to the development build and it worked

khybiske commented 6 years ago

I like Clustal2 the best, in case it is possible to change. I don't like the stacked letter thing at the top (I never like those).

djow2019 commented 6 years ago

Changes now live. You can further tweak the display with the option bar now.

khybiske commented 6 years ago

Outstanding!