Phage evolutionary relationships emerge from protein language model-based proteome representation.

ABSTRACT: Viral taxonomy is a challenging task due to the propensity of viruses for recombination and the lack of universal gene markers. As a result, recent ICTV updates increasingly rely on multiple tools for taxonomic ranking, with a growing emphasis on proteome-based clustering approaches. At the same time, the rapid expansion of viral datasets presents new challenges in organizing, analysing, and discovering phage relationships at scale. To address these challenges, we introduce hierarchical viruses, a framework for comparative genomics of bacteriophages that leverages protein Language Model (pLM) embeddings to generate proteome-wide vector representations of phages. Clustering the vector representations of 24 362 phages from the curated INPHARED dataset reveals a multi-scale hierarchical organ

SUBMITTER: Panigrahi S 

PROVIDER: S-EPMC12541379 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature