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Alternatives to Lollipop for virus variant data

I need to plot amino acid variant locations along a viral gene - I used to use Lollipops (https://github.com/joiningdata/lollipops). MutPlot seems similar (but that's only human data AFAIK https://github.com/VivianBailey/Mutplot)

However since Pfam went over to Interpro, really useful tools like Lollipops no longer work!

Can anyone suggest an R package or a web application that my student can use to make plots like this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5016526/figure/F2/ please?

Thanks!

mutation-plot amino-acid lollipops
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updated by GenoMax GenoMax • written by ch504 • ch504

Do you know what specific information is Lollipop getting from Pfam? Looks like you can still use UniProt. MutPlot appears to be a R-shiny implementation of lollipop so it is the same tool.

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written by GenoMax GenoMax

1 answer

here are a couple of tools i have tagged as 'lollipop' in my awesome-genome-visualization collection

tools tagged lollipop https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Lollipops tools tagged protein https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Protein

an R tool with a lollipop view is trackViewer https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html

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written by cmdcolin cmdcolin

@cmdcolin I think the tool referenced by OP gets the gene info on the fly so it seems attractive to them. Looks like tools you link will simply draw a plot as long as the information is provided up front?

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written by GenoMax GenoMax

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