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Related Concept Videos

Plasmids01:28

Plasmids

51
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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The Replisome03:01

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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
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Updated: Jul 25, 2025

Automated Robotic Liquid Handling Assembly of Modular DNA Devices
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Plassembler: an automated bacterial plasmid assembly tool.

George Bouras1,2, Anna E Sheppard3, Vijini Mallawaarachchi4

  • 1Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.

Bioinformatics (Oxford, England)
|June 27, 2023
PubMed
Summary
This summary is machine-generated.

Plassembler is a new tool that accurately assembles bacterial plasmids from long-read sequencing data, improving upon existing methods. This automated approach reduces the need for manual curation in bacterial genomics research.

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Area of Science:

  • Bacterial genomics
  • Bioinformatics
  • Computational biology

Background:

  • Recent advances in sequencing technologies enable high-quality bacterial chromosome assemblies.
  • Current methods for bacterial plasmid assembly from long-read data are often inaccurate, leading to misassemblies or missed plasmids.
  • Manual curation is frequently required for bacterial plasmid assembly, increasing workload and time.

Purpose of the Study:

  • To develop an automated tool, Plassembler, for accurate bacterial plasmid assembly.
  • To improve upon existing hybrid assembly approaches for bacterial plasmids.
  • To enhance the efficiency and accuracy of bacterial plasmid recovery from sequencing data.

Main Methods:

  • Plassembler utilizes a hybrid assembly approach combining long-read and short-read data.
  • A mapping-based strategy is employed to remove chromosomal reads from the input dataset.
  • The tool is implemented in Python and available as a bioconda package.

Main Results:

  • Plassembler demonstrates increased accuracy in bacterial plasmid assembly compared to the gold standard Unicycler.
  • The tool achieves higher computational efficiency than existing methods.
  • Automated assembly reduces the need for manual intervention and curation.

Conclusions:

  • Plassembler provides an accurate and efficient solution for bacterial plasmid assembly from long-read sequencing data.
  • The tool simplifies and improves the process of bacterial plasmid recovery in genomics.
  • Plassembler is a valuable addition to the bioinformatics toolkit for bacterial research.