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| eggNOG | |
|---|---|
| Name | eggNOG |
| Title | eggNOG |
| Scope | Orthology, functional annotation, phylogenomics |
| Organism | Bacteria, Archaea, Eukaryota, Viruses |
| Center | European Molecular Biology Laboratory |
| Author | Peer Bork |
| Citation | Huerta-Cepas et al. |
eggNOG
eggNOG is a database and resource for orthologous groups and functional annotation used in comparative genomics, metagenomics, and phylogenomics. It integrates large-scale clustering, functional annotation, and hierarchical orthology assignments across viruses, prokaryotes, and eukaryotes to support studies in evolutionary biology and bioinformatics. The resource is widely used by researchers associated with institutions such as the European Molecular Biology Laboratory, the Max Planck Society, the Wellcome Trust, and the European Bioinformatics Institute.
eggNOG organizes protein-coding genes from thousands of genomes into hierarchical orthologous groups to facilitate inference of gene function and evolutionary relationships. The project interfaces conceptually with resources like UniProt, RefSeq, GenBank, Ensembl, and KEGG for sequence sources and annotation transfer. Analysts often combine eggNOG output with tools from BLAST, HMMER, MAFFT, IQ-TREE, and RAxML when constructing phylogenies or performing comparative analyses. Major user communities include researchers from Stanford University, Harvard University, University of Cambridge, Max Planck Institute for Molecular Genetics, and national bioinformatics centers.
The database contains hierarchical orthologous groups spanning taxonomic ranges from domain-specific to phylum- or class-level clusters, linking gene families across model organisms such as Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Arabidopsis thaliana, and representative microbial taxa. Functional annotations map to controlled vocabularies and systems used by Gene Ontology, COG categories, KEGG PATHWAY, and Pfam domains, enabling cross-reference with curated resources like Swiss-Prot, InterPro, and PANTHER. Each orthologous group is described with predicted function terms drawn from evidence lines used in projects at institutions like European Molecular Biology Laboratory and databases such as EggNOG-mapper outputs that are commonly integrated into workflows alongside MetaPhlAn and Anvi'o analyses.
eggNOG's pipeline employs all-against-all sequence comparisons followed by graph-based clustering methods derived from algorithms used in projects at EMBL-EBI and research groups such as those led by Peer Bork and collaborators. The methodology combines pairwise similarity measures produced by tools like DIAMOND or BLAST+ with clustering strategies similar to Markov Cluster Algorithm and summary approaches akin to those used in OrthoMCL and InParanoid. For functional inference, eggNOG integrates domain detection via HMMER against Pfam and consensus annotation strategies inspired by curation procedures at UniProtKB. Phylogenetic reconciliation and orthology/paralogy delineation are informed by techniques employed in studies from University of California, San Diego and Broad Institute groups, using software such as MAFFT and IQ-TREE for tree-based validation.
eggNOG supports applications in genome annotation pipelines at centers like Joint Genome Institute and laboratories conducting metagenomic surveys from projects such as the Human Microbiome Project and Tara Oceans. It is used to assign functions to novel genes in studies from Wellcome Sanger Institute and to explore horizontal gene transfer events discussed in literature affiliated with Max Planck Institute for Evolutionary Anthropology and Cold Spring Harbor Laboratory. Comparative analyses leveraging eggNOG are common in research from University of Oxford, University of Tokyo, ETH Zurich, and University of California, Berkeley; use cases include reconstructing metabolic pathways in studies by groups at Princeton University and mapping gene family expansions reported in work from Columbia University.
Users access eggNOG through web portals and programmatic interfaces developed in tandem with infrastructure at European Bioinformatics Institute and computational platforms like Galaxy and CWL. The eggNOG-mapper tool integrates annotation transfer using fast search engines such as DIAMOND and supports batch annotation workflows deployed on compute clusters at institutions like Argonne National Laboratory and cloud environments used by the National Center for Biotechnology Information. Visualization and downstream analysis often combine eggNOG outputs with pipelines from Cytoscape, MEGA, and Anvi'o to contextualize orthologous groups in network and phylogenetic frameworks.
The project originated from comparative genomics initiatives in European research consortia and has evolved through major releases incorporating genomes and proteomes curated by teams at European Molecular Biology Laboratory, Wellcome Trust Sanger Institute, and collaborating universities. Key contributors and authors have been associated with labs led by Peer Bork and collaborators at institutes including Max Planck Society and CNRS. Successive versions expanded taxonomic coverage and adopted computational improvements paralleling advances made in projects such as UniProt updates and algorithmic innovations from groups at European Bioinformatics Institute.
eggNOG distributes data under licensing terms that facilitate academic use and integration with community resources, with accessibility practices aligned with standards observed by EMBL-EBI and repositories such as NCBI. Datasets and annotation tables are provided for download and programmatic access to support integration into workflows used by research institutions like Harvard Medical School, MIT, and national consortia. Users deploying eggNOG-mapper in commercial settings typically consult institutional policies from organizations such as European Molecular Biology Laboratory and legal offices at contributing universities.
Category:Biological databases