PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets.

ABSTRACT:

Background

Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. Plasmid detection in large genomic datasets is crucial to analyze their spread and quantify their role in bacteria adaptation and particularly in antibiotic resistance propagation. Bioinformatics methods have been developed to detect plasmids. However, they suffer from low sensitivity (i.e., most plasmids remain undetected) or low precision (i.e., these methods identify chromosomes as plasmids), and are overall not adapted to identify plasmids in whole genomes that are not fully assembled (contigs and scaffolds).

Results

We developed PlasForest, a homology-based random forest classifier identifying bacterial plasmid sequences in

SUBMITTER: Pradier L 

PROVIDER: S-EPMC8236179 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature