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YuLab-SMU / ggmsa

:traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2
http://yulab-smu.top/ggmsa
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Protein secondary structure & domain annotation #47

Open gezmi opened 2 years ago

gezmi commented 2 years ago

Hi,

this seems an awesome and very much needed package! I have 2 feature request: would it be possible to add protein secondary structure annotation (helices and beta-sheets) and also domain annotation (similar to the biotite package in python)?

Thank you!

nyzhoulang commented 2 years ago

Hi, @gezmi

I have 2 feature request: would it be possible to add protein secondary structure annotation (helices and beta-sheets) and also domain annotation (similar to the biotite package in python)?

Get it! Thanks for your feedback.
We will try to develop these functions in ggmsa.

Regards, Lang

gezmi commented 2 years ago

Thanks, that would be awesome and much needed! Maybe one more, that I usually miss from MSA visualization tools: the ability to highlight regions with either a) on one/few particular proteins b) all of the proteins. Would this be hard to implement or provide a code with other ggplot function?

orangeSi commented 2 years ago

Thanks, that would be awesome and much needed! Maybe one more, that I usually miss from MSA visualization tools: the ability to highlight regions with either a) on one/few particular proteins b) all of the proteins. Would this be hard to implement or provide a code with other ggplot function?

explore the msa maybe easier by html like this: https://orangesi.github.io/pymsaploter/ (support mark domain location and search by motif pattern)

m3hdad commented 1 year ago

feature request seconded!

eernst commented 1 year ago

Thirded! Domain annotation plotting would be fantastic.

gnxsf commented 1 month ago

Any update on this feature request? Adding domain annotation would be very useful!