EggNOG-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
Details and methodology about the tool and its database are best explained on their website: http://eggnogdb.embl.de/#/app/methods.
EggNOG-mapper can be found under Functional Analysis → EggNOG Annotation → EggNOG Mapper. The wizard allows to select the parameters for the functional annotation (figure 1).
Target Orthologs: Define what type of orthologs should be used for functional transfer.
GO Evidence: Define what type of GO terms should be used for annotation:
experimental = Use only terms inferred from experimental evidence.
non-electronic = Use only non-electronically curated terms.
Figure 1. EggNOG Mapper wizard page.
The result table summarizes all annotations that could be transferred with EggNOG Mapper. Besides ordering and filtering, the context menu allows to take a closer look at certain results (figure 2). This annotation process also generates a Summary Report with information about the total number of GOs, the COG categories and the orthologous groups distribution.
Figure 2. EggNOG results table.
The annotation details (right-click on an annotated sequence → Show Annotation Details) provide link outs where possible and give detailed information about annotated GOs (figure 3).
Figure 3. Annotation details.
Merge EggNOG Annotations
Once the sequences are annotated via EggNOG, it is possible to merge the GO terms and the EC codes (Enzyme Commission Codes) to a sequence project in order to add the new annotations. This can be done by clicking on Functional Analysis → EggNOG Annotation → Merge EggNOG GO Annotations (figure 4).
In the wizard, you have to select the sequences project to merge the GO annotations to. If the sequences already have annotated GO terms and/or ECs, the new information generated from EggNOG will be added to the annotations found in the project.
In addition, you can filter the annotations by E-value or Bit-Score.
Figure 4. Merge EggNOG GO Annotations wizard.
Once finished, this step generates a barchart showing the total number of GOs and ECs added to the original sequence project (figure 5).
Figure 5. Merge EggNOG GO Annotations graph.
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Jaime Huerta-Cepas, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering and Peer Bork. Submitted (2016).
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, Mathias C. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, and Peer Bork. Nucl. Acids Res. (04 January 2016) 44 (D1): D286-D293. doi: 10.1093/nar/gkv1248