EggNOG-mapper

EggNOG-mapper performs rapid functional annotation of novel sequences by transferring functional information from precomputed orthologous groups and phylogenies in the eggNOG database.

Key Features:

• Orthology-based functional annotation: Assigns functions via fine-grained orthology assignments using precomputed clusters and phylogenies from the eggNOG database to reduce misannotations from close paralogs.
• Performance: Reports substantially higher speed and accuracy than conventional methods, running approximately 15× faster than BLAST and at least 2.5× faster than InterProScan.
• Validation and benchmarking: Demonstrated top-5 performance in all three Gene Ontology categories on the CAFA2 NK-partial dataset and showed reduced false positive assignments with increased recovery of experimentally validated terms.
• Version 2 enhancements: Integrates eggNOG v5 databases, supports de novo gene prediction from raw contigs, includes built-in pairwise orthology prediction, provides fast protein domain discovery, and performs automated GFF decoration.

Scientific Applications:

• Genome, transcriptome and metagenomic annotation: Functional annotation of novel genomes, transcriptomes, and metagenomic gene catalogs.
• Clinical microbial genomics: Functional profiling and annotation in clinical microbial genomics studies.
• Functional evolution studies: Inference of functional evolution using orthology-based annotation transfer.
• Microbiological research: Large-scale functional annotation for diverse microbiological research areas.

Methodology:

Uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional annotations via fine-grained orthology assignments; includes de novo gene prediction from raw contigs, pairwise orthology prediction, protein domain discovery, and automated GFF decoration.