Empathi: embedding-based phage protein annotation tool by hierarchical assignment.

ABSTRACT: Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of protein sequences. Consequently, the majority of functions carried by phage proteins remain elusive. Current tools to comprehensively identify phage protein functions from their sequence either lack sensitivity (those relying on homology for instance) or specificity (assigning a single coarse grain function to a protein). Here, we introduce Empathi, a protein-embedding-based classifier that assigns functions in a hierarchical manner. New categories were specifically elaborated for phage protein functions and organized such that molecular-level

SUBMITTER: Boulay A 

PROVIDER: S-EPMC12521583 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature