eggNOG

eggNOG provides orthology assignments, functional annotations, and evolutionary relationships for genes across diverse taxa to support comparative genomics and metagenomics analyses.


Key Features:

  • Orthologous Groups (OGs): OGs are constructed using reciprocal best BLAST matches, triangular linkage clustering, and hierarchical consistency algorithms, comprising over 17 million OGs computed at 1,601 taxonomic levels across bacteria (10,756 species), archaea (457 species), eukaryotes (1,322 species), and viruses.
  • Functional Annotations: Functional annotations integrate KEGG, Gene Ontology terms, UniProtKB, BiGG, CAZy, CARD, PFAM, and SMART domain information, with eggNOG 6.0 achieving approximately 80% annotation coverage.
  • Phylogenetic Analysis: Precomputed maximum-likelihood trees per OG enable investigation of duplication and speciation events and derivation of pairwise orthology relationships within OGs.
  • Precomputed HMM Profiles: Precomputed HMM profiles are provided for OGs to support sequence annotation and functional assignment of novel sequences.
  • Methodological Enhancements: Non-supervised clustering on extensive genome datasets and construction of nested orthologous groups (NOGs) support propagation of functional terms across hierarchical groups.

Scientific Applications:

  • Comparative Genomics: Accurate orthologous group assignments across species for comparative genomic analyses.
  • Functional Annotation of Novel Sequences: Annotation of novel protein sequences using precomputed HMM profiles and phylogenetic trees.
  • Phylogenetic Profiling: Investigation of evolutionary histories and distribution of functional terms within OGs.
  • Single-Copy OG Identification: Identification of single-copy OGs at custom taxonomic levels to support studies of gene evolution and speciation.

Methodology:

Reciprocal best BLAST matches, triangular linkage clustering, hierarchical consistency algorithms, non-supervised clustering, construction of nested orthologous groups (NOGs), precomputed HMM profiles, and maximum-likelihood phylogenetic tree inference.

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Topics

MetagenomicsGenomics

Collections

de.NBI

Details

License:
GPL-3.0
Maturity:
Mature
Cost:
Free of charge
Tool Type:
web application
Operating Systems:
Linux, Windows, Mac
Programming Languages:
Python
Added:
2/11/2016
Last Updated:
11/24/2024

Operations

Publications

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. 2011;40(D1):D284-D289. doi:10.1093/nar/gkr1060. PMID:22096231. PMCID:PMC3245133.

PMID: 22096231
PMCID: PMC3245133

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research. 2009;38(suppl_1):D190-D195. doi:10.1093/nar/gkp951. PMID:19900971. PMCID:PMC2808932.

PMID: 19900971
PMCID: PMC2808932

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research. 2015;44(D1):D286-D293. doi:10.1093/nar/gkv1248. PMID:26582926. PMCID:PMC4702882.

PMID: 26582926
PMCID: PMC4702882

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research. 2007;36(Database):D250-D254. doi:10.1093/nar/gkm796. PMID:17942413. PMCID:PMC2238944.

PMID: 17942413
PMCID: PMC2238944

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research. 2013;42(D1):D231-D239. doi:10.1093/nar/gkt1253. PMID:24297252. PMCID:PMC3964997.

PMID: 24297252
PMCID: PMC3964997

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research. 2018;47(D1):D309-D314. doi:10.1093/nar/gky1085. PMID:30418610. PMCID:PMC6324079.

PMID: 30418610
PMCID: PMC6324079
Funding: - Horizon 2020: 686070 - Ramón y Cajal Programme: RYC-2016-20621 - Fondo Social Europeo: PEJ-2017-AI/TIC-7514 - Novo Nordisk Foundation: NNF14CC0001 - Bundesministerium für Bildung und Forschung: #031A537B - Swiss National Science Foundation: 31003A-160095

Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research. 2022;51(D1):D389-D394. doi:10.1093/nar/gkac1022. PMID:36399505. PMCID:PMC9825578.

PMID: 36399505
PMCID: PMC9825578
Funding: - National Programme for Fostering Excellence in Scientific and Technical Research: PGC2018-098073-A-I00 MCIU/AEI/FEDER - Chan Zuckerberg Initiative: 2020-218584 - Severo Ochoa Centres of Excellence Programme from the State Research Agency (AEI) of Spain: 2017–2021, SEV-2016–0672 - Research Technical Support Staff Aid: PTA2019-017593-I/AEI/10.13039/501100011033 - Novo Nordisk Foundation: NNF14CC0001

Documentation

General
http://eggnogdb.embl.de/#/app/methods

Downloads

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