Biological foundation models illuminate annotation blind spots in evolutionarily divergent genomes (opens in new tab)

Chromosome-scale assemblies are increasingly available for non-model organisms, but functional annotation remains limited when deep evolutionary divergence erodes primary amino-acid sequence identity even though protein structural similarity can remain conserved. We present a hybrid annotation framework that decouples gene-model discovery from cross-species similarity assignment by combining Evo2-based ab initio prediction of exon-intron structures with ESM-2 protein-embedding-based structura...