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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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Can i use eggnog to predict both orthologues and paralogues, or orthologues only? #464

Open timeresistance1996 opened 1 year ago

Cantalapiedra commented 1 year ago

Hi @timeresistance1996 ,

This is an interesting question, but I am afraid that the straightforward answer would be "none of them". EggNOG is a database of groups of orthologues (OGs). However, when you use eggNOG-mapper you are not retrieving the actual orthologues of your query. Instead, you are retrieving the orthologues of the "seed ortholog" which is the target of the hit obtained with diamond, mmseqs or hmmer.

If you mean whether you can obtain the paralogues of the seed ortholog, I am not sure, but I would say only in-paralogues using the option --target_orthologs https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.10#annotation-options

For instance, if I am not mistaken, using --target_orthologs one2many you will retrieve the orthologs along with the in-paralogs. However, my guess is that other kind of paralogues will belong to other OGs, and in those cases you will not be retrieving them.

Best, Carlos

timeresistance1996 commented 1 year ago

Thank you for your answer. I have got it！