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Related Concept Videos

Plasmids01:28

Plasmids

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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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Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Related Experiment Video

Updated: Oct 11, 2025

Plasmid Stability Analysis with Open-Source Droplet Microfluidics
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Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.

William B Andreopoulos1,2, Alexander M Geller3, Miriam Lucke3

  • 1Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA.

Nucleic Acids Research
|December 6, 2021
PubMed
Summary
This summary is machine-generated.

Deeplasmid, a new deep learning tool, accurately distinguishes bacterial plasmids from chromosomes using DNA sequence data. This advancement aids in discovering novel plasmid-borne genes and understanding microbial evolution.

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Area of Science:

  • Microbial genomics
  • Bioinformatics
  • Molecular evolution

Background:

  • Plasmids are crucial mobile genetic elements facilitating horizontal gene transfer, particularly for antimicrobial resistance.
  • Short-read sequencing of microbial genomes often yields mixed contigs from both plasmids and chromosomes.
  • Accurate plasmid identification tools are essential for discovering novel plasmid-borne genes and understanding microbial ecology.

Purpose of the Study:

  • To develop a deep learning tool, Deeplasmid, for accurate differentiation of bacterial plasmids from chromosomes.
  • To provide a robust method for identifying plasmid-borne genes and novel plasmids from assembled genomic sequences.

Main Methods:

  • Developed Deeplasmid, a deep learning model utilizing DNA sequence and encoded biological data.
  • Input sequences can be generated by any sequencing platform and assembly algorithm.
  • Evaluated Deeplasmid's performance against five other plasmid classification methods.

Main Results:

  • Deeplasmid achieved an AUC-ROC of over 89%, outperforming existing methods.
  • The tool's runtime scales linearly with the number of assembled sequences.
  • Successfully predicted a novel 102 kb plasmid in *Yersinia ruckeri* ATCC 29473, later validated by long-read sequencing.

Conclusions:

  • Deeplasmid offers a highly accurate and efficient deep learning approach for plasmid identification.
  • The tool facilitates the discovery of previously unknown plasmids and their associated genes.
  • This advancement has significant implications for microbial ecology, evolution, and the study of antimicrobial resistance.