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
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.