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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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Emapper online - NOG name instead of top hit? KO instead of map? #25

Closed courtneystairs closed 7 years ago

courtneystairs commented 8 years ago

Hi Jamie,

I was wondering if there is a mapping file of eggNOG where I could relate the top hit back to the actual NOG name + number (rather than the accession number for that particular protein).

Furthermore, is there a mapping file to go from the eggNOG number to the KEGG orthology rather than the map number?

Are these options implemented in the stand-alone version?

Thank you very much for your help :) Courtney

jhcepas commented 8 years ago

Hi Courtney, The "members.tsv" files in the download section ( http://eggnogdb.embl.de/#/app/downloads) provides content information of each eggNOG group (both number of members, species and actual list of accessions). If the taxonomic scope of your searches are not restricted, you may need to download the member files for all taxonomic levels.

Regarding KEGG KOs, no, this is not available yet, but we are woking on expanding the functional database sources and KOs will be included in next releases.

On 10 October 2016 at 15:25, courtneystairs notifications@github.com wrote:

Hi Jamie,

I was wondering if there is a mapping file of eggNOG where I could relate the top hit back to the actual NOG name + number (rather than the accession number for that particular protein).

Furthermore, is there a mapping file to go from the eggNOG number to the KEGG orthology rather than the map number?

Are these options implemented in the stand-alone version?

Thank you very much for your help :) Courtney

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jhcepas/eggnog-mapper/issues/25, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJ_Sn4MI0k42dWkQA9WiSVSrdohU-z-ks5qyjzNgaJpZM4KSj8X .

rohansachdeva commented 7 years ago

I think the file "eggnog4.protein_id_conversion.tsv.gz" from the FTP provides mappings to KEGG IDs. You could then use the KEGG API To get the KOs for each ID.

@jhcepas does that sound right?

jhcepas commented 7 years ago

That's right, but it is an old conversion and not sure how much work would require using the KEGG API. KO mappings are close to be ready in the main branch so, if possible, I would suggest to wait until they are officially integrated.

On 24 April 2017 at 22:21, Rohan Sachdeva notifications@github.com wrote:

I think this file "eggnog4.protein_id_conversion.tsv.gz" from the FTP provides mappings to KEGG IDs. You could then use the KEGG API To get the KOs for each ID.

@jhcepas https://github.com/jhcepas does that sound right?

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jhcepas commented 7 years ago

KO modules feature request issue: #43

rohansachdeva commented 7 years ago

Are the mappings in "eggnog4.protein_id_conversion.tsv.gz" to RefSeq up to date? Because they could be used to pull KOs from the KEGG API.

jhcepas commented 7 years ago

not really, refseq ids are two or three years old at least.