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

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 assignmen...

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Published inMolecular biology and evolution Vol. 38; no. 12; pp. 5825 - 5829
Main Authors Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Letunic, Ivica, Bork, Peer, Huerta-Cepas, Jaime
Format Journal Article
LanguageEnglish
Published United States Oxford University Press 09.12.2021
Subjects
Annotations
Databases, Genetic
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Genes
Genomics
Metagenome
Metagenomics
Molecular Sequence Annotation
Orthology
Phylogeny
Predictions
Resources
Software
computational genomics
metagenomics
bioinformatics
functional annotation
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Summary: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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ISSN:1537-1719
0737-4038
1537-1719
DOI:10.1093/molbev/msab293