ArticleNucleic acids research2023
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed.
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- Whole-genome analysis of Pantoea alfalfae HF1 isolated from shot hole lesions in peach leaves and symptom reproduction by wound inoculation.AMB Express · 2026Article
- Decoding the human gut bacterial plasmids in colorectal cancer.Communications biology · 2026Article
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- Cross-Host Adaptation ofMicroorganisms · 2026Article
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- Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.Environmental microbiome · 2026Article
- Genomic characterization of clinical Stenotrophomonas strains from Thailand reveals five putative novel genospecies and extensive functional diversity.Scientific reports · 2026Article
- Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Origin of replication discovery for environmentally isolatediScience · 2026Article
- Distinct ESBL dissemination mechanism associated with the hybrid transposon TnMicrobiology spectrum · 2026Article
- PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment.Genome biology · 2026Article
- Unraveling the activity of phage-carrying antibiotic resistance genes in constructed wetlands.Frontiers in cellular and infection microbiology · 2026Article
- Advances in deep learning for antimicrobial research.Frontiers in microbiology · 2026Review
- The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A Monitoring Method to Evaluate the Accumulation of Antimicrobial-Resistance Genes in Gram-Negative Bacteria Distributed in Environmental Water.Environmental microbiology reports · 2025Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Streptomyces shaoguanensis sp. nov.: elucidating the mechanisms of efficient chicken feather degradation and its potential for biofertilizer development.Microbial cell factories · 2025Article
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4 authors.
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Abstract
Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.
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