How does MetaProdigal handle metagenomics where different genetic codes are used?
I’m wondering how prodigal when using -p meta can handle genes from different genetic codes? For example, if Gracilibacteria/SR1 was in there it would use genetic code 25. Would it catch this? When running in meta mode does it end up using the genetic code translation table argument?
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My understanding: Prokka will by default use translation table 11. It tries to detect codon usage and may switch to table 4 automatically. You should see a warning if the tool cannot make sense of the input with either. As far as i know there is no autodetection for other tables. You can use the argument
-g 25 to specify table 25 manually. I don’t know a prodigal-only solution for when your Gracilibacteria are part of a metagenome, though. You would have to do some taxonomic binning first (which is recommended before prodigal usage anyways).
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