To do this, it is necessary to have previously mapped your sequences (via BLAST search) to the RefSeq COG and KOG databases integrated in the NCBI Conserved Domain Database (CDD) (Schug et al. 2002) available at the FTP of the NCBI. For details about how to perform a BLAST search, see the section “BLAST and HMM Pipeline”.
Once you have the CSV resulting from the COG/KOG automatic annotation, you can use the Worksheet utility “Annotation” to add COG or KOG terms to your CSV by clicking on the tabs “Append COG terms” (if you are annotating prokaryotic orthologs) or “Append KOG terms” (if you are dealing with eukaryotic orthologs) by choosing the column of reference (“GI”) and the type of data contained in this column (“GI” or “Protein names”). Finally, check the boxes below this dialog to choose the COG/KOG terms you want to append to the worksheet by adding two or three new columns and click OK.