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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
- 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
[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
Or, if you use the novel families database instead of eggNOG 5, please cite:
[2] Functional and evolutionary significance of unknown genes from uncultivated taxa. Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Carlos P. Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Lucas Paoli, Thomas S.B. Schmidt, Shinichi Sunagawa, Peer Bork, Luis Pedro Coelho, Jaime Huerta-Cepas. 2022. bioRxiv 2022.01.26.477801. https://doi.org/10.1101/2022.01.26.477801
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Depending on the tools used, you may want to cite also:
* HMMER
Accelerated Profile HMM Searches. Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195.
* Diamond
Sensitive protein alignments at tree-of-life scale using DIAMOND. Buchfink B, Reuter K, Drost HG. 2021. Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
* MMseqs
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988
* Prodigal
Prodigal: prokaryotic gene recognition and translation initiation site identification. Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119.
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Original eggNOG-mapper 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).