MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model.

ABSTRACT:

Background

Mobilization typing (MOB) is a classification scheme for plasmid genomes based on their relaxase gene. The host ranges of plasmids of different MOB categories are diverse, and MOB is crucial for investigating plasmid mobilization, especially the transmission of resistance genes and virulence factors. However, MOB typing of plasmid metagenomic data is challenging due to the highly fragmented characteristics of metagenomic contigs.

Results

We developed MOBFinder, an 11-class classifier, for categorizing plasmid fragments into 10 MOB types and a nonmobilizable category. We first performed MOB typing to classify complete plasmid genomes according to relaxase information and then constructed an artificial benchmark dataset of plasmid metagenomic fragments (PMFs) from t

SUBMITTER: Feng T 

PROVIDER: S-EPMC11299106 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature