Layers/Functional-annotations.md

@@ -4,6 +4,7 @@ title: Functional annotations
 
 
 
+
 Functional annotation helps bringing biological meaning to genetic sequences. Functional annotation is usually obtained through protein sequence similarity. Indeed, across two organisms, if two sequences are very similar, one can infer that they can encode for the same biological function.
 There are several main parameters that will impact the process of functional annotation:
 - how distant is the species which was actually annotated with experimental data (the reference)
@@ -22,6 +23,7 @@ The annotation tool EggNOG-mapper (https://github.com/eggnogdb/eggnog-mapper) re
 First, install emapper, which can be done for example with conda:
 
 `conda create -n emapper -c bioconda eggnog-mapper`
+_Note that the version 2.1.12 does not currently work (https://github.com/eggnogdb/eggnog-mapper/issues/516). While the issue is not fixed, please use `conda create -n emapper_2.1.12 -c bioconda -c conda-forge eggnog-mapper=2.1.12 python=3.11.10`_
 
 Then create the eggNOG database which contains ortholog groups and the functional annotation. In our case, we will chose the taxonomic group Viridiplantae, whose code is 33090 (see [http://eggnog5.embl.de/#/app/downloads](http://eggnog5.embl.de/#/app/downloads))