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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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How to use smart annotation mode in local eggnog-mapper #384

Open wook2014 opened 2 years ago

wook2014 commented 2 years ago

I have noticed that eggnog-mapper server online (http://eggnog-mapper.embl.de/) can use smart annotation to form a output file. How could I use smart annotation when I run eggnog-mapper on my local server?

wook2014 commented 2 years ago

Another question is that what is the output file format for? There is no table header in the file to annotate what the data is for each column. I can only recognize that the first column is the fasta file gene name of my gene and a very important result for the second column seemed to be common used gene name, but not everyone can be properly found in NCBI. Is there any official documents that can be referred to?

Cantalapiedra commented 2 years ago

Hi @wook2014 ,

I am afraid that you cannot use smart annotation with the standalone version. It is only available online. Regarding the output, I would say that the fields are:

Basically, as in Figure 1 here https://academic.oup.com/nar/article/46/D1/D493/4429069

Regarding the 2nd column, they are domain names from SMART. For example http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=PBPb

Also, for further info check https://academic.oup.com/nar/article/49/D1/D458/5940513 and references therein.

Best, Carlos