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Overview

EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed Orthologous Groups (OGs) and phylogenies from the EggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.

Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.

The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).

Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan are available here.

EggNOG-mapper is also available as a public online web resource: http://eggnog-mapper.embl.de

Documentation

Current versions

• eggNOG-mapper (2.1.5 - 2.1.6)
• eggNOG-mapper Web
• FAQ - Frequently Asked Questions

Previous versions

• eggNOG-mapper (2.1.2 - 2.1.4)
• eggNOG-mapper (2.1.0 - 2.1.1)
• eggNOG-mapper (2.0.2 - 2.0.8)
• eggNOG-mapper (2.0.0 - 2.0.1)
• eggNOG-mapper v1

Citation

[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain                                                                         
      prediction at the metagenomic scale. Carlos P. Cantalapiedra,                                                                                    
      Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas.                                                                               
      biorxiv (2021). doi: https://doi.org/10.1101/2021.06.03.446934

[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
      orthology resource based on 5090 organisms and 2502 viruses. Jaime
      Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia
      K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars
      J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8;
      47(Database issue): D309–D314. doi: 10.1093/nar/gky1085 

Original paper:

    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).