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functional-annotation

separate

Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.

When to use

• adding functional annotation to predicted genes
• choosing between eggNOG-mapper and InterProScan
• judging how much to trust a functional label
• assigning GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names
• reconciling orthology and domain signature evidence
• annotating bacterial isolates, eukaryotic proteomes, and metagenomes
• handling twilight-zone or ORFan proteins with ML or structure-based methods

When not to use

• using DIAMOND-vs-Swiss-Prot alone for GO annotation
• treating domain presence as proof of specific function
• ignoring provenance and evidence tiering in annotation

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