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

Abstract

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.

Subspecies in the global human gut microbiome

“…For the functional characterization of subspecies, we annotated the genes to functional categories (Materials and Methods) and ascertained whether these were specific to either SC or SSSC, by testing for enrichment of functional annotations such as SEED (Overbeek et al , 2005) pathways, eggNOG (Huerta‐Cepas et al , 2016b) categories, and KEGG (Kanehisa & Goto, 2000) modules in all the species with subspecies structure (Fig EV3). Compared to the combined SCs, the combined SSSCs were enriched in genes functionally related to phages (including genes for integration and excision), cell surface protein modifications (such as genes from the sortase pathway), chemotaxis, and motility as well as genes of unknown function (Table EV6).…”

“…Annotation of the reconstructed gene complements was transferred from a published annotation of the IGC (Kultima et al , 2016). From this study, we specifically used annotations to eggNOG (Huerta‐Cepas et al , 2016b), KEGG (Kanehisa & Goto, 2000), and SEED (Overbeek et al , 2005) as indicated in the main text.…”

De novo assembly and characterization of the Hucho taimen transcriptome

“…The transcript and protein sequences of brown trout, brook trout, and grayling were downloaded from the PhyloFish database (Pasquier et al., 2016). The eggNOG database (Huerta‐Cepas et al., 2016) was used to define the gene family, and eggNOG‐mapper was used to search the fiNOG dataset for orthologous groups (Huerta‐Cepas et al., 2017). To reconstruct the species tree and calculate the divergence time, single‐copy gene families were extracted and the protein sequences were aligned with MUSCLE.…”

Comparative Computational Analysis of a Putative Transcriptional Regulator Map_PRSO3010 and its implications in the Pathogenesis of Crohn’s and Johne’s diseases

“…EggNOG [16] an orthology prediction methodology employing Graph-based method was employed to search for an ortholog of the Rv0757 (phoP) gene in MAP genome.…”