pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences.

Abstract

MOTIVATION: The increasing number of fully sequenced bacterial plasmids being annotated and catalogued has prompted the development of computational tools for comparing and classifying them. Existing approaches typically compare full-length DNA sequences (e.g. Mash, BLASTn, and ANI-based methods) or translated open reading frames (ORFs) (e.g. DIAMOND), with plasmid-level scores obtained by aggregating ORF-to-ORF similarities; however, they are either restricted to closely related plasmids or become computationally demanding in large-scale analyses. RESULTS: We describe pLAST (plasmid Language Analysis and Search Tool), a plasmid-search tool built using word2vec representations of protein-family content informed by local genomic context. Benchmarks indicate that pLAST outperforms nucleotide-based methods and performs comparably to DIAMOND in identifying functionally similar plasmids and compared with the widely used Mash, it achieves 26% and 24% improvements in detecting shared mating-pair formation system type and relaxase type, respectively. This performance scales to database searches across hundreds of thousands of sequences, as demonstrated using the precomputed PlasmidScope collection of ∼750 000 plasmids. Beyond global similarity, pLAST also returns per-ORF plasmid-plasmid alignments, enabling detection of shared functional modules. AVAILABILITY AND IMPLEMENTATION: pLAST is freely accessible as a web server at https://plast.lbs.cent.uw.edu.pl/ or https://plast.lbs.biol.uw.edu.pl/ and available as a Python module along with a precomputed database at https://github.com/labstructbioinf/pLAST for customized analysis.