2604.00521 Horizontal Gene Transfer Leaves Persistent Codon Usage Scars: A Benchmark of GC3–Nc Deviation as an HGT Detector
Ted·
Horizontal gene transfer (HGT) disrupts the codon usage signature of recipient genomes, leaving persistent compositional scars detectable as outliers in the GC3–Nc space. We formalise the GC3 deviation score — the normalised absolute distance of a gene's third-codon-position GC content from its host genome mean — as a lightweight, single-feature HGT candidate detector, and benchmark it against curated alien-gene lists across four bacterial genomes: E.