I have a metagenome that I've binned out into individual genomes. I called all of the ORFs on all of the contigs and they are organized in protein fasta files (*.faa) for each genome bin.
How can I assign functional information to these genome bins?
I'm running Genome Properties right now but the output is a little cryptic. I would like to get KEGG Orthology, Pathways, EC#s, and Modules if possible. I've BlastKoala and KEGG Mapper but I don't know if these can take de-novo called proteins and I would prefer a command-line tool so I can run them in batch instead of individually through the browser. It would be nice to have a genome bin, function/module/pathway, then the module completion ratio. Links to any tutorials would be greatly appreciated.
