ArticleBMC bioinformatics2021
PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 51 citations in OpenAlex.
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- The planktonic microbiome of the Great Barrier Reef.Nature · 2026Article
- Antarctic soil microbiomes encode structurally conserved and phylogenetically diverse beta-lactamases.iMetaOmics · 2026Article
- Comparative Genome Analysis and Characterization of Lacticaseibacillus Paracasei NKN344 Strain Isolated from Curd of Buffalo Milk Reared on Brackish Water Lagoons of the Eastern Indian Coast.Probiotics and antimicrobial proteins · 2026Article
- Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.Microbiome · 2026Article
- Comparative genomic insights into the genus Pantoea: genetic determinants of ecological lifestyle diversity and plant growth-promoting potential.World journal of microbiology & biotechnology · 2026Article
- Long-term spatiotemporal dynamics of β-lactamase resistome in the Han River, South Korea.Frontiers in microbiology · 2026Article
- PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning.Briefings in bioinformatics · 2024Article
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases.Nature communications · 2024Article
- MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model.GigaScience · 2024Article
- Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota.Frontiers in genetics · 2024Article
- Plasmid genomic epidemiology ofAntimicrobial agents and chemotherapy · 2023Article
- Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.Nature communications · 2023Article
- Article
- Global transmission of broad-host-range plasmids derived from the human gut microbiome.Nucleic acids research · 2023Article
- PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.Nucleic acids research · 2023Article
- The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria.Microbiology spectrum · 2023Article
- Article
- plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.Frontiers in microbiology · 2023Article
- Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
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Abstract
backgroundPlasmids 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).
resultsWe developed PlasForest, a homology-based random forest classifier identifying bacterial plasmid sequences in partially assembled genomes. Without knowing the taxonomical origin of the samples, PlasForest identifies contigs as plasmids or chromosomes with a F1 score of 0.950. Notably, it can detect 77.4% of plasmid contigs below 1 kb with 2.8% of false positives and 99.9% of plasmid contigs over 50 kb with 2.2% of false positives.
conclusionsPlasForest outperforms other currently available tools on genomic datasets by being both sensitive and precise. The performance of PlasForest on metagenomic assemblies are currently well below those of other k-mer-based methods, and we discuss how homology-based approaches could improve plasmid detection in such datasets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.