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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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What KEGG .pep files do DRAM devs use for KEGG.pep (and others if they want to comment!) #325

Open caity-s opened 6 months ago

caity-s commented 6 months ago

Dear DRAM team and others,

We just got our KEGG subscription - there are a lot of .pep files there.

I can see from issues #305 and #182 that concatenation of the ftp.kegg.net/kegg/genes/organisms//pep.gz files has been an options, but I look at kegg/genes/fasta/prokaryotes.pep.gz and think surely that has all the proks, so maybe combine with the euk and virus .pep files (except this doesn't have the kff files... so perhaps that is why concatenated organism .pep files are chosen)?

What does the DRAM team use these days (e.g. for their DRAM2 preps)?

Thanks for the tips,

Caitlin