blast against KOG database

Question

[seta]

Hi all,

Please help me with homology search of a de novo assembled transcriptome against KOG database. I searched on the net a lot, but I did not find any complete tutorial or documentation about it. Any suggestion and hand experience from you about KOG annotation would be really welcomed.

Thanks in advance

Answer 1

[Philipp Bayer]

You can find a fasta of the 2014 update of the COGs here: ftp://ftp.ncbi.nih.gov/pub/COG/COG2014/data/

Homepage: http://www.ncbi.nlm.nih.gov/COG/

The old 2003 KOGs are here: ftp://ftp.ncbi.nih.gov/pub/COG/KOG/

From there you can extract and run BLAST manually, or you can run the COGs software (README int he tar): ftp://ftp.ncbi.nih.gov/pub/COG/KOG/

[seta]

Thank you for your response. I am familiar with the locally running blast (say blastp, blastx), but I heard that RPS-Blast has to be used for this homology search. After downloading the fasta file of 2014 update COG, could you please tell me how to make blast database and do this kind of blast, my mean is what the right commands are for this purpose?