eggNOG-mapper v2

eggNOG-mapper v2 annotates genes and predicts functional annotations for genomic and metagenomic sequences using orthology-based transfers, protein domain discovery, de novo gene prediction, and automated GFF decoration.

Key Features:

• Precomputed Orthology Assignments: Uses precomputed orthologous groups and phylogenies from the eggNOG database (v5) to transfer functional information via fine-grained orthologs.
• De Novo Gene Prediction: Performs de novo gene prediction directly from raw contigs to generate gene models for annotation.
• Pairwise Orthology Prediction: Provides built-in pairwise orthology prediction to infer functions by comparing individual gene pairs across species.
• Fast Protein Domain Discovery: Employs efficient algorithms for rapid identification and annotation of conserved protein domains.
• Automated GFF Decoration: Automatically adds functional annotations to General Feature Format (GFF) files for downstream analyses.

Scientific Applications:

• Genomic and Metagenomic Workflows: Generates rapid functional annotations for single genomes and complex metagenomic assemblies to support downstream analyses.
• Comparative Genomics Studies: Enables evolutionary and orthology-based analyses by providing pairwise and ortholog-group-based functional inferences across species.
• Functional Genomics Research: Supports discovery of gene function and protein domain architecture through integrated annotation and domain detection.

Methodology:

Integrates precomputed orthologous groups and phylogenies from the eggNOG database with de novo gene prediction and pairwise orthology analysis to transfer functional annotations to novel sequences.