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wilkox / gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
http://wilkox.org/gggenes
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would be nice for protein people #70

Open AnnaPagotto opened 9 months ago

AnnaPagotto commented 9 months ago

Hi David,

I ran into this amazing package, and since I'm more of a protein person, I was wondering if you could make something similar to represent protein domains and secondary structure.

Pasted Graphic

Let me know if this is in your plans :)

Thank you and all the best,

Anna

wilkox commented 9 months ago

I'm currently working on implementing all the Sequence Features from the SBOL Visual Specification 3.0.0 [PDF] in gggenes. These are for nucleic acids but there might be some overlap which is useful to you. The development version of this is in the SBOL_glyphs branch.

If you know of any similar specification for representing protein features please let me know and I'll consider adding it after the SBOL glyphs (or perhaps a separate ggprotein?)

AnnaPagotto commented 9 months ago

I'm not aware of any similar document containing specifications for the representation of protein features, but there is a worldwide accepted notation system called "Richardson ribbon diagram" from Jane Richardson (https://doi.org/10.1016/S0065-3233(08)60520-3).

The three main class of secondary structure for proteins are helix, strand and turn (this is the annotation that is also used in UniProt, from where one can retrieve the information on the secondary structure). In the ribbon representation alpha helices are typically depicted as coiled ribbons (springs), while beta strands are shown as arrows, where the the arrowhead points toward the C-terminus of the protein (hence the arrows are always forward). Turns are instead represented as a straight line.

It would very cool and useful to have a ggprotein extension!

Let me know if you are interested in this, I would be happy to discuss further!