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dasmoth / dalliance

Interactive web-based genome browser.
http://www.biodalliance.org/
BSD 2-Clause "Simplified" License
226 stars 68 forks source link

Feature request: gene overview #63

Open parlar opened 10 years ago

parlar commented 10 years ago

A useful thing would be an overview pane of genes. It could be used for orientation (highlightening current exon you are looking at) but also for quick navigation between different exons within a gene. Exon numbers could perhaps also be displayed in popups, or provided below or above.

I don't know how difficult it would be to implement such a feature?

mdrasmus commented 10 years ago

@dasmoth Could the chains configuration be used to create a genome where the introns are "spliced-out"? Then all exons would be contiguous and every other track would plot its data in spliced coordinates. This would be vary nice for visualizing exonic variants and understanding where in the protein product the change is made (near the end or near a splice junction), without large introns squishing all exons to being only pixels wide.

cc @ymen

ymen commented 10 years ago

@dasmoth We also briefly discussed this issue on the Dalliance Google group. https://groups.google.com/forum/#!topic/biodalliance-dev/6yBxQBUO2TA

I have not revisited the problem with greater details, but if you have any tips or suggestions on how to proceed (or let me know the dumb mistakes I'm making) that would be really helpful! :)

dasmoth commented 10 years ago

Yes, I think the coordinate mapping approach is the right way to go. Not entirely sure what's going wrong for @ymen but will take a look ASAP.