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塑镜:一个全面的等离子体数据库,有丰富的注释和在线分析工具

Yinhu Li^1,2,3, Xikang Feng^4,5, Xuhua Chen²

¹CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.

Nucleic acids research

|October 23, 2024

概括

"PlasmidScope"是一个新的数据库,为超过85万个等离子体提供了全面的注释和分析. 这个资源使研究人员能够通过先进的可视化工具探索等离子体的多样性和功能.

科学领域:

微生物学微生物学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

等离子体是外染色体遗传元素,对于水平基因转移至关重要.
现有的等离子体数据库缺乏全面的标准化和注释.
需要一个统一的资源来管理不断增长的等离子体序列数据量.

研究的目的:

介绍PlasmidScope,一个新的,全面的,注释的等离子体数据库.
为研究人员提供用于等离子体研究的先进分析和可视化工具.

主要方法:

从10个存储库整理了852,600个质粒.
集成了12个最先进的注释工具.
利用9个数据库进行功能基因注释和ESMFold进行蛋白质结构预测.

主要成果:

塑镜提供了广泛的注释,包括基因组完整性,拓,移动性,宿主和遗传元素 (tRNA,tRNA,CRISPR/Cas).
为超过2500万个预测的基因提供功能注释.
包括预测的蛋白质结构用于增强分析.

结论:

塑镜作为一个有价值的,塑研究的综合资源.
该数据库通过自动化分析和可视化,促进了对等离子体生物学的深入探索.

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相关概念视频

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...