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).
EggNOG-mapper is also available as a public online resource: http://beta-eggnogdb.embl.de/#/app/emapper.
https://github.com/jhcepas/eggnog-mapper/wiki
If you use this software, please cite:
[1] 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).
[2] 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