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

Author:

Cantalapiedra Carlos P1ORCID,Hernández-Plaza Ana1,Letunic Ivica2,Bork Peer345,Huerta-Cepas Jaime1

Affiliation:

1. Centro de Biotecnologia y Genomica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, Madrid, Spain

2. Biobyte Solutions GmbH, Heidelberg, Germany

3. European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany

4. Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany

5. Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea

Abstract

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.

Funder

National Programme for Fostering Excellence in Scientific and Technical Research

Severo Ochoa Centres of Excellence Programme

State Research Agency

Research Technical Support Staff Aid

European Research Council

BMBF

Publisher

Oxford University Press (OUP)

Subject

Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics

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4. The Gene Ontology Resource: 20 years and still GOing Strong;Nucleic Acids Res,2018

5. Advances and applications in the quest for orthologs;Glover;Mol Biol Evol,2019

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