Urgent please help. Can single proteins that are not shared between plasmids be called their own protein orthogroups? ?
For simplicity sake, I have two plasmid sequences made up of three and four protein coding regions respectively.
There are two protein orthogroups between my two plasmids (coding sequences 1 and 1 of each plasmid make up the first orthogroup and coding sequences 2 and 2 of each plasmid make up the second orthogroup)
I want to know if the remaining 3 sequences not shared between the two plasmids comprise their own protein orthogroups and so become orthogroup 3, orthogroup 4 and orthogroup 5?
Please help :(
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