# eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

“eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale” (2021), by Carlos P. Cantalapiedra et al. Genetics and Biochemistry research paper. Original abstract below, unchanged. A free PDF is available.

- Authors: Carlos P. Cantalapiedra, Ana Hernández-Plaza, Ivica Letunić, Peer Bork B, Jaime Huerta‐Cepas
- Published: September 30, 2021
- Field: Genetics and Biochemistry
- DOI: https://doi.org/10.1093/molbev/msab293
- Free PDF: https://www.biorxiv.org/content/biorxiv/early/2021/06/04/2021.06.03.446934.full.pdf

## Abstract

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.

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