Question: About The Cog Table For Complete Microbial Genome On Ncbi
3
gravatar for Cindy
8.4 years ago by
Cindy60
Cindy60 wrote:

On the NCBI website,there's a COG table for each complete microbial genome,as shown below:

The COG table of Acaryochloris marina MBIC11017

But I can't figure out what (% in sequence) (% in genome) (% in genus) (% in Cyanobacteria) and (% in Bacteria) in this table refer to respectively in this table. I can't go on with statistical analysis without knowing the exact meaning of those data. I hope someone could help me with this one.

ncbi classification functional • 3.0k views
ADD COMMENTlink modified 8.4 years ago by Neilfws48k • written 8.4 years ago by Cindy60
4
gravatar for Neilfws
8.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Unfortunately, there is very little help or documentation available for the COG database. We are reduced to educated guess-work.

Taking the top row, COG J, I'd guess that:

  • % in genus = percentage of proteins from Acaryochloris that are COG J
  • % in Cyanobacteria = percentage of proteins from phylum Cyanobacteria that are COG J
  • % in Bacteria = percentage of proteins from kingdom Bacteria that are COG J

The first 2 columns are less obvious. I'd guess that "% in sequence" might be based on a sum of sequence lengths (coding?) and "% in genome" is percentage of proteins from that genome, but it is not clear at all.

Having said all that: I would not use COG - it is a very old database and is no longer maintained by the NCBI. You can get similar information from KEGG or the IMG (Integrated Microbial Genomes).

ADD COMMENTlink written 8.4 years ago by Neilfws48k
1

Have a look at this page for Acaryochloris marina MBIC11017 - http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641228474. If you scroll down there are COGs, KEGG, MetaCyc and a bunch of other useful and exciting stuff.

ADD REPLYlink written 8.4 years ago by Neilfws48k

Thanks.KEGG and IMG may provide much more infomation.As I'm still not familiar with these databases,I wonder if there's a tool which can do functional clustering of all genes from a specific complete microbial genome,just like COG table. Coz I'm focusing on the statistial analysis of the functional clusters among different species,rather than the functional content of a specific genome.

ADD REPLYlink written 8.4 years ago by Cindy60

Thanks.KEGG and IMG may provide much more infomation.As I'm still not familiar with these databases,I wonder if there's a tool which can do functional clustering of all genes from a specific complete microbial genome,just like COG table. Coz I'm focusing on the statistial analysis of the functional clusters among different species,rather than the functional content .

ADD REPLYlink written 8.4 years ago by Cindy60

I've just read that page and found a bunch of useful tools.Thanks a lot for helping me.

ADD REPLYlink written 8.4 years ago by Cindy60
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