Question

how to assign COGs to my genome?

0

Entering edit mode

7.5 years ago

sidrairshad29 • 0

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?

genome software error • 3.5k views

ADD COMMENT • link updated 7.5 years ago by colindaven 6.3k • written 7.5 years ago by sidrairshad29 • 0

0

Entering edit mode

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

ADD REPLY • link 7.5 years ago by dago ★ 2.8k

score 0 · Answer 1 · 2016-10-20

0

Entering edit mode

7.5 years ago

Farbod ★ 3.4k

Dear sidrairshad29, Hi

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

~ Best

ADD COMMENT • link 7.5 years ago by Farbod ★ 3.4k

score 0 · Answer 2 · 2016-10-20

0

Entering edit mode

7.5 years ago

dago ★ 2.8k

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 COMMENT • link 7.5 years ago by dago ★ 2.8k

score 0 · Answer 3 · 2016-10-20

0

Entering edit mode

7.5 years ago

colindaven 6.3k

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 COMMENT • link 7.5 years ago by colindaven 6.3k

0

Entering edit mode

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

ADD REPLY • link 7.5 years ago by GenoMax 141k

0

Entering edit mode

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.