Question: blast against KOG database
1
gravatar for seta
3.0 years ago by
seta1.1k
Sweden
seta1.1k wrote:

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

blast alignment kog annotation • 2.2k views
ADD COMMENTlink modified 3.0 years ago by Philipp Bayer6.0k • written 3.0 years ago by seta1.1k
0
gravatar for Philipp Bayer
3.0 years ago by
Philipp Bayer6.0k
Australia/Perth/UWA
Philipp Bayer6.0k wrote:

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/

ADD COMMENTlink written 3.0 years ago by Philipp Bayer6.0k

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?

ADD REPLYlink written 3.0 years ago by seta1.1k
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