ArticleBioinformatics (Oxford, England)2020
PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Predicting the bacterial host range of plasmid genomes using the language model-based one-class support vector machine algorithm.Microbial genomics · 2025Article
- Deep learning methods in metagenomics: a review.Microbial genomics · 2024Review
- Deep learning in microbiome analysis: a comprehensive review of neural network models.Frontiers in microbiology · 2024Review
- Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu.World journal of microbiology & biotechnology · 2023Article
- More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome.Frontiers in cellular and infection microbiology · 2022Article
- VirionFinder: Identification of Complete and Partial Prokaryote Virus Virion Protein From Virome Data Using the Sequence and Biochemical Properties of Amino Acids.Frontiers in microbiology · 2021Article
- The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment.Water research X · 2020Review
- Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures.Microbial genomics · 2020Article
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Authors and funding
7 authors.
Funding
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Abstract
summaryWe present the first tool of gene prediction, PlasGUN, for plasmid metagenomic short-read data. The tool, developed based on deep learning algorithm of multiple input Convolutional Neural Network, demonstrates much better performance when tested on a benchmark dataset of artificial short reads and presents more reliable results for real plasmid metagenomic data than traditional gene prediction tools designed primarily for chromosome-derived short reads. AVAILABILITY AND IMPLEMENTATION: The PlasGUN software is available at http://cqb.pku.edu.cn/ZhuLab/PlasGUN/ or https://github.com/zhenchengfang/PlasGUN/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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