Questions tagged [eggnog]

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Error with eggNOG-mapper jobs

I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the 'Orthogroup_Sequences' which contains a huge list of protein files in fasta ...
K_081's user avatar
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2 votes
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COG Enrichment, the overrepresentation test between annotated transcriptome and a set of annotated gene, eggnog-mapper annotation results

I am dealing with a transcriptome of a species and list of genes selected for a gene enrichment analysis. In order to see what kind of genes in my selected list are overrepresented compared with the ...
se-tima's user avatar
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1 vote
1 answer
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Fisher's exact test for COG categories in pan, core genome analysis

I have come across several papers that do a Fisher's exact test to show over represented genes in COG categories specifically in a pan-core-accessory-species specific genome analysis. The test is done ...
K_081's user avatar
  • 117
1 vote
1 answer
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eggNOG: DNA-DNA or protein-protein orthologue identification?

I'm trying to work out is how reliable/accurate my eggNOG metagenomic outputs are. Critical for this is how its identifying orthologues. Background eggNOG is ...
M__'s user avatar
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1 vote
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eggNOG API, how's it work?

Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
M__'s user avatar
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