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Related Concept Videos

Plasmids01:28

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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PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools.

Yinhu Li1,2,3, Xikang Feng4,5, 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.

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|October 23, 2024
PubMed
Summary

PlasmidScope is a new database that offers comprehensive annotations and analysis for over 850,000 plasmids. This resource empowers researchers to explore plasmid diversity and function through advanced visualization tools.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Plasmids are extrachromosomal genetic elements crucial for horizontal gene transfer.
  • Existing plasmid databases lack comprehensive standardization and annotation.
  • A need exists for a unified resource to manage the growing volume of plasmid sequence data.

Purpose of the Study:

  • To introduce PlasmidScope, a novel, comprehensive, and annotated plasmid database.
  • To provide researchers with advanced analytical and visualization tools for plasmid research.

Main Methods:

  • Curated 852,600 plasmids from 10 repositories.
  • Integrated 12 state-of-the-art annotation tools.
  • Utilized 9 databases for functional gene annotation and ESMFold for protein structure prediction.

Main Results:

  • PlasmidScope provides extensive annotations including genome completeness, topology, mobility, host, and genetic elements (tRNA, tmRNA, CRISPR/Cas).
  • Offers functional annotations for over 25 million predicted genes.
  • Includes predicted protein structures for enhanced analysis.

Conclusions:

  • PlasmidScope serves as a valuable, integrated resource for plasmid research.
  • The database facilitates in-depth exploration of plasmid biology through automated analysis and visualization.