Leveraging Natural Language Processing models to decode the dark proteome across the Animal Tree of Life

Functional annotation is crucial in biology, but many protein-coding genes remain uncharacterized, especially in non-model organisms. FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) integrates protein language models for large-scale functional annotation. Applied to ∼1,000 animal proteomes, it predicts functions to virtually all proteins, revealing previously uncharacterized functions that enhance our understanding of molecular evolution. FANTASIA is available on GitHub at https://github.com/CBBIO/FANTASIA .