Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Abstract

Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g., new assignments only available through database updates), less precise homology-based functional transfer is still the default for (meta-)genome annotation. We, therefore, developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database. To validate our method, we benchmarked Gene Ontology (GO) predictions against two widely used homology-based approaches: BLAST and InterProScan. Orthology filters applied to BLAST results reduced the rate of false positive assignments by 11%, and increased the ratio of experimentally validated terms recovered over all terms assigned per protein by 15%. Compared with InterProScan, eggNOG-mapper achieved similar proteome coverage and precision while predicting, on average, 41 more terms per protein and increasing the rate of experimentally validated terms recovered over total term assignments per protein by 35%. EggNOG-mapper predictions scored within the top-5 methods in the three GO categories using the CAFA2 NK-partial benchmark. Finally, we evaluated eggNOG-mapper for functional annotation of metagenomics data, yielding better performance than interProScan. eggNOG-mapper runs ∼15× faster than BLAST and at least 2.5× faster than InterProScan. The tool is available standalone and as an online service at http://eggnog-mapper.embl.de.

De novo assembly and characterization of the Hucho taimen transcriptome

“…Meanwhile, the COG functional category annotation using eggNOG‐mapper (Huerta‐Cepas et al., 2017) yielded good results and a total of 72,605 putative proteins. These COG‐annotated putative proteins were successfully classified into 125 COG functional categories, and most were homologous to 32 molecular families, including signal transduction mechanisms, transcription, post‐translational modification, cytoskeleton, and intracellular trafficking and secretion (Figure 4).…”

“…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.…”

Meta-analysis of the General Coral Stress Response:Acroporacorals show opposing responses depending on stress intensity

“…Gene annotations were acquired using eggNOG-mapper (http://eggnogdb.embl.de/#/app/ emapper ; Huerta-Cepas et al 2017;Huerta-Cepas et al 2019). This produced GO, COG, and KEGG and gene names (eggnog annotations).…”

Transcriptional response of the obligate anaerobe Desulfuribacillus stibiiarsenatis MLFW‐2T to growth on antimonate and other terminal electron acceptors

“…Genes were considered to be differentially transcribed between the two growth conditions if they had a |fold change| ≥ 2 and an adjusted p-value ≤ 0.05. Differentially transcribed genes were annotated using the eggNOG-mapper (Huerta-Cepas et al, 2017).…”