EGGNOG Automatic Classification based on COG categories

eggNOG database (version 5.0.2)

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a public resource in which thousands of genomes are analyzed at once to establish orthology relationships between all their genes.

eggNOG focuses on providing: (i) comprehensive functional annotations for the inferred orthologs, (ii) predictions across thousands of genomes covering the three domains of life and viruses, and iii) hierarchical resolution of orthology assignments and fine-grained relationships (i.e. in-paralogies) based on phylogenetic analysis.

An Orthologous Group (OG) is defined as a cluster of three or more homologous sequences that diverge from the same speciation event.

Orthologous Groups were functionally annotated using updated versions of Gene Ontology, KEGG pathways, SMART/PFAM domains and expanded to CAZy and KEGG modules. Moreover, general free text descriptions and COG functional categories were updated for each OG.

More information about the method: http://eggnogdb.embl.de/#/app/methods

Reference: eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Jaime Huerta-Cepas, Damian Szklarczyk & al. Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D309–D314.

eggNOG-mapper (version 2.1.12)

eggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database 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).

We run eggnog-mapper using EGGNOGDB and diamond for the alignement.

More information about eggNOG-mapper: http://eggnog-mapper.embl.de/

Reference: 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).

EGGNOG Automatic Classification page

This page presents statistics on reference genome genes classified by eggNOG in Orthologous Groups (OG) by COG functional categories.

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  • COG Process: COG functional process name.

  • COG Category: COG functional category ID.

  • COG Category Description: COG functional category description.

  • CDS: Number of the CDSs classified by eggNOG in at least one COG category.

  • %: Percentage of the CDSs classified by eggNOG in at least one COG category.

Clicking on a COG category displays all genes assigned to OG in that COG functional category.

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  • OG ID: eggNOG Orthologous Group id.

  • OG function: eggNOG Orthologous Group functional description.

  • Label: Label of the protein. If you click on the label, you access to the Gene annotation window.

  • Gene: Gene name of the protein if any.

  • Product: Product description of the protein.

  • COG: Clusters of Orthologous Group name (COG).

  • PFAM short name: InterPro PFAM entry name.

  • KO: KEGG Ortholog entry ID.