EggnogGenome uses best BLAST hit and the Eggnog database to annotate functions on a query set of proteins. Eggnog uses the COG functions notation

Expected workflow:

1. Download Eggnog database. Required files are:
   • eggnog4.proteins.core_periphery.fa.gz: protein FASTA that will be used as BLAST database
   • data/NOG/NOG.members.tsv.gz: table mapping Eggnog proteins to their COG function(s)
2. Transform the Eggnog proteins FASTA into BLAST database. Eg: makeblastdb -dbtype prot -in eggnog4.proteins.core_periphery.fa -out eggnog.blastdb
3. BLASTp your query proteins against Eggnog BLAST database. Eg:
   • Legacy BLAST: blastall -p blastp -d eggnog.blastdb -i query_proteins.fa -o matches.blast -e .01 -m 7 -a 60 -K 1
   • BLAST+: blastp -db eggnog.blastdb -query query_proteins.fa -out matches.blast -evalue .01 -max_hsps 1 -outfmt 5 -num_alignments 1 -num_threads 60
4. Run eggnog_genome.py

Links:

Eggnog homepage

Eggnog downloads

NCBI BLAST