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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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CDS glyph #320

Open rbuels opened 11 years ago

rbuels commented 11 years ago

Make a CDS glyph that displays frame, phase, and translated AA sequences, depending on magnification. Simliar to http://search.cpan.org/~lds/Bio-Graphics-2.37/lib/Bio/Graphics/Glyph/cds.pm from GBrowse.

Also make the ProcessedTranscript glyph use them instead of just plain boxes for CDS regions.

rbuels commented 11 years ago

Be careful to handle the pathological case mentioned in http://gmod.827538.n3.nabble.com/CDS-glyph-sequence-changes-when-spanning-introns-td1007897.html

selewis commented 11 years ago

I would say that for displaying the frame that the color coded method used by Apollo works very well (Designed by biologists). Can we talk more to spec this out, not sure the current GBrowse approach is yet ideal.

-S

On Aug 16, 2013, at 12:03 PM, Robert Buels notifications@github.com wrote:

By careful to handle the pathological case mentioned in http://gmod.827538.n3.nabble.com/CDS-glyph-sequence-changes-when-spanning-introns-td1007897.html

— Reply to this email directly or view it on GitHub.

rbuels commented 11 years ago

On 08/16/2013 03:34 PM, selewis wrote:

I would say that for displaying the frame that the color coded method used by Apollo works very well (Designed by biologists). Can we talk more to spec this out, not sure the current GBrowse approach is yet ideal.

Could you write down the color-coding semantics from Apollo here?

cmdcolin commented 6 years ago

The color coding of cds frame can be done in jbrowse-land using https://github.com/cmdcolin/colorbycds