bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization
Human milk glycan (HMG) metabolism, especially by Bifidobacteria, is crucial for infant gut colonization and healthy microbiome development. The enzymes involved in HMG metabolism often have many non-HMG-related homologs, necessitating fine-grained annotation for accurate assessment of bifidobacterial HMG metabolic capabilities. However, current annotation tools provide only broad glycoside hydrolase (GH) family classifications. We present bifidoAnnotator, a tool for fine-grained annotation and visualization of bifidobacterial GH genes involved in HMG utilization. bifidoAnnotator leverages MMseqs2 to map protein sequences against a manually curated database of over 22000 bifidobacterial GH proteins organized into 13 families and 122 functional clusters with experimental validation status. The tool performs hierarchical annotation at family and cluster levels, identifying specific homologous protein variants rather than just broad family assignments, and generates publication-ready heatmaps for comparative analysis.  Availability and implementation. The bifidoAnnotator's source code and documentation is hosted at GitHub (https://github.com/nicholaspucci/bifidoAnnotator.git). bifidoAnnotator is installable via conda.