Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

By Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, C. von Mering, Peer Bork. 2016

2,475 citations recorded by the source corpus.

Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines relatively in accessible, less precise homology-based functional transfer is still the default for (meta-)genome annotation. We therefore developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from eggNOG. To validate our method, we benchmarked Gene Ontology predictions against two widely used homology-based approaches: BLAST and InterProScan. Compared to BLAST, eggNOG-mapper reduced by 7% the rate of false positive assignments, and increased by 19% the ratio of curated terms recovered over all terms assigned per protein. Compared to InterProScan, eggNOG-mapper achieved similar proteome coverage and precision, while predicting on average 32 more terms per protein and increasing by 26% the rate of curated terms recovered over total term assignments per protein. Through strict orthology assignments, eggNOG-mapper further renders more specific annotations than possible from domain similarity only (e.g. predicting gene family names). eggNOG-mapper runs ~15x than BLAST and at least 2.5x faster than InterProScan. The tool is available standalone or as an online service at http://eggnog-mapper.embl.de.

Subfields: Molecular Biology

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “0 has also improved the underlying precomputed data used by the online version of eggNOG-mapper (40), a tool for rapid annotation of custom (meta-)genomes.”
MGnify: the microbiome analysis resource in 2020 (2019, neutral): “0.3) (44).”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, positive): “For the functional proﬁles shown in Figures 3E and 5E, we used the Brite Hierarchy from KEGG to screen metabolic related pathways and KOs among all the KOs annotated by EggNOG.”
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, neutral): “In the same spirit as the mapping tool of the EggNOG database (34), we now provide a feature to annotate custom protein sequences through a fast approximate search with all the sequences in OMA.”
Advances and Applications in the Quest for Orthologs (2019, methodology): “mapper algorithm (Huerta-Cepas et al. 2017) for inferring function on a genomic scale using pairwise orthology predic-”
PANNZER2: a rapid functional annotation web server (2018, methodology): “Despite not being entered into CAFA, we included eggNOGmapper due to its reported high-performance and scalability (13).”
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome (2018, background): “12.6 ( Huerta-Cepas et al., 2016 ) outputs for our genes with the program ‘anvi-import-functions’ to import annotations from other databases, including PFAM ( Bateman et al., 2004 ), and eggNOG ( Jensen et al., 2008 ).”