eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
By C. Cantalapiedra, Ana Hernández-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. bioRxiv, 2021
4,097 citations recorded by the source corpus.
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: (i) de novo gene prediction from raw contigs, (ii) built-in pairwise orthology prediction, (iii) fast protein domain discovery, and (iv) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/f37aa684501336b9e3121743bd7e926b443cc8c5
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Citations in the corpus
- Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum (2023, methodology): “14.5 (Seemann, 2014) with specific parameters ('—metagenome’) then annotated by KOfam and custom HMM profiles within METABOLIC v.4.0 (Zhou et al., 2022) and eggNOG-emapper v.2.1.2 (Cantalapiedra et al., 2021) with default settings.”