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Thanks very much, but this only gives some bacterial enzymes that can cut my protein, unfortunately.
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The breseq pipeline is a good start
https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing
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Not as comprehensive as above but there is also `pepdigest` from EMBOSS: https://www.bioinformatics.nl/cgi-bin/emboss/pepdigest
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Have you tried PeptideCutter? https://web.expasy.org/peptide_cutter/
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There were two opinions about this in a past thread: https://www.biostars.org/p/9575107/
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Is there anyone that can help me?
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I've just added a [relevant comment there][1] in case anyone comes across the topic.
[1]: https://www.biostars.org/p/77372/#9611355
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Thank you so much for this! I am going to add some print calls and see, as well as a toy snakefile.
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You can post screenshots of plots you have questions about.
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