Predicting stop codon reassignment improves phage genome annotation: Pharokka-gv and Prokka-gv (ISME Communications)

The study predicted 76 INPHARED genomes and 712 Unified Human Gut Virome Catalogue vOTUs that repurpose a stop codon to encode an amino acid, and re-annotated them with modified Pharokka-gv and Prokka-gv tools. For sequences predicted to reassign TAG to glutamine, Pharokka-gv raised median gene length by 67.8% (UHGV) and 72.9% (INPHARED) and increased median coding capacity to about 90%.