Question: how to assign COGs to my genome?
0
gravatar for sidrairshad29
2.5 years ago by
sidrairshad290 wrote:

hello members i want to assign Clusters Of orthologous Groups of functions to my newly sequenced and annotated genome and want to get a pie graph of this how i can?

software error genome • 1.4k views
ADD COMMENTlink modified 2.5 years ago by colindaven1.2k • written 2.5 years ago by sidrairshad290

In general if you google a bit you will find all the answers you need.

ADD REPLYlink written 2.5 years ago by dago2.5k
0
gravatar for Farbod
2.5 years ago by
Farbod3.2k
Toronto
Farbod3.2k wrote:

Dear sidrairshad29, Hi

please have a look at on line COG analysis and this post (for bar chart, of course).

~ Best

ADD COMMENTlink written 2.5 years ago by Farbod3.2k
0
gravatar for dago
2.5 years ago by
dago2.5k
Germany
dago2.5k wrote:

I guess this is the official program to use : https://sourceforge.net/projects/cogtriangles/files/ And you should use the newest version of the db form 2015

ADD COMMENTlink written 2.5 years ago by dago2.5k
0
gravatar for colindaven
2.5 years ago by
colindaven1.2k
Hannover Medical School
colindaven1.2k wrote:

What I've heard before and is backed up by this link COGs is that COGs are really, really old. Why not use Interproscan, available as command line software in Java, or over the web interface at the EBI ?

Otherwise more recent databases would be a better bet, perhaps Tigrfams or similar. I personally really like Interpro though as it queries many, many databases chiefly using HMMs.

ADD COMMENTlink written 2.5 years ago by colindaven1.2k

@Dago links COG paper from 2015 while the latest COG data available at NCBI is from late 2014.

ADD REPLYlink written 2.5 years ago by genomax65k

Paper was published in January 2015, and it was "First published online: November 26, 2014". I guess that the most recent DB is the one from the 2014.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by dago2.5k

I guess COG is more comprehensive than Tigrfam.

ADD REPLYlink written 2.5 years ago by dago2.5k
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