Find out if a protein has an ortholog in EggNog DB
1
0
Entering edit mode
5.9 years ago
peter pfand ▴ 110

Hi,

I have a list of human genes for which I want to check whether there are orthologs in Bacteria. For this purpose, I've decided to make use of the EggNog DB, but when I see the files I get lost. Could anyone tell me how to check if an ortholog group in human or a given human protein is in an ortholog group of bacteria?

Are the protein names in EggNog in different formats?

eggnog orthologs human • 1.8k views
ADD COMMENT
0
Entering edit mode

Did you figure this out?

ADD REPLY
0
Entering edit mode
3.8 years ago
urema • 0

Hi,

Seen your post and I was wondering if you ever figured this out?

I am attempting to use eggNOG and its methods offline to extract orthologous proteins etc. However it seems as though no-one wants to participate in problem-solving !

If you want we can discuss this stuff, as I know how to work with eggNOG through its online interface, yet have trouble attempting to replicate its HMM creation etc.

Thanks, U.

ADD COMMENT
0
Entering edit mode

Hi urema, no, I did not. I sent an email to the first author off the eggNOG paper but he never replied... so I took an alternative approach.

ADD REPLY

Login before adding your answer.

Traffic: 1881 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6