Peter Vegh

Finally, you can also save the plot in a vector graphics format (svg) and use an image editor (Inkscape) to change the text.

Please find the publication here: https://www.biorxiv.org/content/10.1101/2020.01.09.900589v1 'Citation Tools' on the right.

DNA Features Viewer has been published in Bioinformatics: Zulkower and Rosser (2020), _DNA Features Viewer: a sequence annotation formatting and plotting library for Python._ Bioinformatics, Volume 36, Issue 15, 1...

Thank you, I have not used plotly or dash before, but DNA Features Viewer uses matplotlib and perhaps these links will help: [SO Question](https://stackoverflow.com/questions/49851280/showing-a-simple-matplotlib-plot-in-plotly-dash), https://github.com/plotly/dash/issues/250

Thank you @gjerman , that is useful. Then to obtain a species table, it just needs adding the translation column and calculating the % to get a format as in...

Thanks for the details; if I search for a species with the web interface, there is an option to return a table, and that has percentages as well. But maybe...

I can confirm your issue. This is the best answer I could find: https://stackoverflow.com/questions/19098518/how-to-download-a-file-perl-cgi-backend-using-python-requests?noredirect=1&lq=1 A better solution seems to be to download the whole dataset instead, and subset that for...

That works for me, thanks

The documentation you refer to is: https://edinburgh-genome-foundry.github.io/DnaChisel/ref/builtin_specifications.html?highlight=codon_usage_table#avoidrarecodons DNA Chisel uses this repository for codon tables: https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables An example table: https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/blob/master/codon_usage_data/tables/e_coli_316407.csv As you can see, frequencies add up to 1, separately...

Thanks very much, this is an interesting synthesis constraint that may need to be added. I'll try / look into your suggestion sometime during this week.