eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

By Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, M. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn and 3 more. 2015

1,948 citations recorded by the source corpus.

eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes (2019, background): “As a result, most mainstream phylogenomic databases, such as Ensembl [12] , EggNOG [13] , OrthoDB [14] , or OMA [15] do not provide phylogenetic profiles.”
OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, background): “Some of the best established orthology resources include EggNOG (Huerta-Cepas et al., 2016) , Ensembl Compara (Zerbino et al., 2018) , Inparanoid (Sonnhammer and Östlund, 2015) , MBGD (Uchiyama et al., 2012) , OrthoDB (Zdobnov et al., 2017) , OrthoMCL (Chen et al., 2006) , Panther (Mi et al., 2017) ”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “…uniparc_all.xml.gz) such as functional, phylogenomic, and protein domain annotations (KEGG, KO, EggNOG, GO, EC, Pfam) (El-Gebali et al., 2019; Huerta-Cepas et al., 2016; Kanehisa and Goto, 2000; The Gene Ontology Consortium, 2019) , accessions for cross-referencing entries with external…”
20 years of the SMART protein domain annotation resource (2017, methodology): “Protein orthology data are parsed from the the eggNOG database version 4.5 (19) and covers ∼ 7.5 million proteins from > 3500 species.”
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier (2017, methodology): “…to protein sequences, we use protein-protein interaction (PPI) networks for multiple species from the STRING database [26], filtered by confidence score of 300 and connected with orthology relations from the EggNOG database [18] by creating a symmetric ortholog-of edge for each orthology group.”
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.”
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline (2018, methodology): “Currently, three different Diamond runs are performed: against the GenBank nr database for taxonomic assignment, against the eggNOG database (Huerta-Cepas et al., 2016) for COG/NOG annotation, and against the latest publicly available version of KEGG database (Kanehisa and Goto, 2000) for KEGG ID an”