I am assigning COG categories to proteins of newly seqeunced bacterial genomes.
To do that I am using COGNITOR in the COGsoft.
I used the protein sequences and the other files available on the NCBI ftp server, for creating the blastDB and creating the "seqeunce universe" requested by the program.
Following the isntructions I got stuck in the last step where the program COGcognitor is called. This is what reported in the manual:
"To run COGNITOR you need a COG domain assignment file (as described in 2.10.). If your file is called COGs.csv, the following command will be used:
$ COGcognitor -i=./BLASTcogn -t=COGs.csv -q=GenQuery.p2o.csv -o=GenQuery.COG.csv # COGNITOR results in GenQuery.COG.csv"
I cannot understand the nature of the file COGs.csv. Has it the format <protein_ID>,<COG_category>?
If yes, can use the "whog" file in the COG section of the NCBI ftp server to create the COGs.csv?
Honestly, I find the instruction of the program quite hard to interpret.