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Plasmids

Plasmids

Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...

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相关实验视频

Updated: Sep 12, 2025

Plasmid Stability Analysis with Open-Source Droplet Microfluidics

Plasmid Stability Analysis with Open-Source Droplet Microfluidics

Published on: December 27, 2024

等离子体:一种用于等离子体序列预测的新型管道.

Rosalia Palomino-Cabrera¹, Inmaculada Garcia Romero², Miguel A Valvano³

¹Servicio de Microbiología H. U. Marqués de Valdecilla - IDIVAL, Santander, Spain.

Studies in health technology and informatics

|August 8, 2025

概括

PLASMIDITY是一种新的机器学习管道,用于检测等离子体DNA序列. 它可以从全基因组测序 (WGS) 数据中准确识别等离子体,改进了现有的等离子体预测工具.

关键词:

抗菌药物反症 (AMR) 是一种生物信息学是一种生物信息学.机器学习机器学习塑体塑体塑体

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

相关实验视频

Last Updated: Sep 12, 2025

Plasmid Stability Analysis with Open-Source Droplet Microfluidics

Plasmid Stability Analysis with Open-Source Droplet Microfluidics

Published on: December 27, 2024

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
计算生物学计算生物学

背景情况:

等离子体DNA对于细菌适应和抗生素耐药性至关重要.
从全基因组测序 (WGS) 数据中准确检测等离子体仍然具有挑战性.
现有的工具往往缺乏全面的特征分析,以进行可靠的等离子体识别.

研究的目的:

开发和验证PLASMIDITY,一个用于等离子体序列检测的自动化管道.
利用机器学习来增强等离子体结合的特征.
提高在基因组数据集中识别等离子体DNA的准确性和效率.

主要方法:

PLASMIDITY集成连接组装与机器学习分类器 (渐变增强).
分析的特征包括结合长度,多重性,圆性和遗传标记 (等离子体和染色体).
该管道使用k-mer配置文件和与等离子体参考数据库进行相似性搜索.

主要成果:

训练有素的梯度提升分类器在模拟的WGS数据上获得了0.901的F1最高得分.
该管道在200个分类学上不同的样本上进行了训练和测试.
与其他等离子体预测工具相比,PLASMIDITY表现出更好的性能.

结论:

PLASMIDITY为等离子体序列检测提供了一个强大的,自动化的解决方案.
机器学习方法有效地利用了各种序列和标记特征.
该工具增强了在基因组研究中对等离子体传播的特征的分析.