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GMOD
CDS glyph
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.
Be careful to handle the pathological case mentioned in http://gmod.827538.n3.nabble.com/CDS-glyph-sequence-changes-when-spanning-introns-td1007897.html
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 [email protected] 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
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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?
The color coding of cds frame can be done in jbrowse-land using https://github.com/cmdcolin/colorbycds
