ProFIT v2.0.0: Species-specific Prophage Fingerprint Reference Databases

ProFIT v2.0.0: Species-specific Prophage Fingerprint Reference Databases This dataset contains species-specific prophage fingerprint reference databases developed for ProFIT (Prophage Fingerprint-based Identification and Typing), version 2.0.0. The release provides databases for five bacterial species: Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter hormaechei. Each species-specific database includes four core files: reference_strain_metadata.tsv: Reference strain metadata, including sequence type (ST) information. reference_strain_vOTU_matrix.feather: Binary prophage vOTU presence–absence profiles of reference strains. vOTU_metadata.tsv: Mapping of individual prophage sequences to their corresponding vOTUs. vOTU_members.fna.gz: Nucleotide sequences of all prophage members assigned to the reference vOTUs. All member sequences within each vOTU are retained to support sequence-level matching and subsequent vOTU assignment. ProFIT uses these assignments to construct prophage fingerprints and compare query genomes with reference strains using Jaccard similarity. Each bacterial species is distributed as a separate downloadable archive, allowing users to install only the reference database relevant to their analysis. Database manifests and file checksums are provided to support integrity verification and reproducible analyses. The databases are designed for use with ProFIT v2.0.0. See the accompanying software documentation for installation instructions, analysis methods, and interpretation of target-species database matching.