Find out if a protein has an ortholog in EggNog DB

Question

[Juan Cordero]

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?

[urema]

Did you figure this out?

Answer 1

[urema]

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.

[Juan Cordero]

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.