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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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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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Bacterial identification relies on a diverse array of techniques to classify and understand microorganisms, each tailored to uncover specific characteristics. Traditional morphological approaches, while still valuable, are limited for closely related or structurally simple organisms. Modern methods integrate biochemical, serological, genetic, and advanced molecular tools to achieve greater accuracy.Morphological and Biochemical TechniquesMorphological characteristics, such as cell shape and...
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Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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Updated: Sep 20, 2025

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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Current Methods for Recombination Detection in Bacteria.

Anton E Shikov1,2, Yury V Malovichko1,2, Anton A Nizhnikov1,2

  • 1Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.

International Journal of Molecular Sciences
|June 10, 2022
PubMed
Summary
This summary is machine-generated.

Genetic exchange, including homologous recombination (HR) and horizontal gene transfer (HGT), drives bacterial evolution. This review classifies and summarizes bioinformatics tools for detecting these crucial genetic events.

Keywords:
HGT detectionhomologous recombination (HR)horizontal gene transfer (HGT)phylogenetic methodsrecombination detectionsynteny

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Area of Science:

  • Microbiology
  • Genetics
  • Bioinformatics

Background:

  • Genetic exchange mechanisms like homologous recombination (HR) and horizontal gene transfer (HGT) are fundamental to bacterial evolution and adaptation.
  • Numerous bioinformatics tools exist for detecting recombination and HGT, but a systematic review of their capabilities and limitations is lacking.
  • Existing tools often focus on either HR or HGT, despite underlying algorithmic similarities and interconnected evolutionary roles.

Purpose of the Study:

  • To systematically review and classify existing bioinformatics tools for detecting genetic exchange events in bacteria.
  • To provide a comprehensive overview of methodologies for identifying homologous recombination and horizontal gene transfer.
  • To highlight the pros and cons of various tools based on the genomic consequences of recombination.

Main Methods:

  • Classification of bioinformatics tools based on the genomic consequences of recombination.
  • Systematic review of existing software for detecting homologous recombination (HR) and horizontal gene transfer (HGT).
  • Analysis of the types of traceable events targeted by different detection programs.

Main Results:

  • Dozens of bioinformatics tools are available for detecting recombination and HGT.
  • Tools can be broadly categorized based on their focus: HR or HGT, though methods share algorithmic foundations.
  • A systematic classification and comparison of these tools, considering their specific applications, is presented.

Conclusions:

  • Understanding the strengths and weaknesses of different bioinformatics tools is crucial for accurate detection of genetic exchange.
  • A unified approach to classifying tools based on genomic outcomes can aid researchers in selecting appropriate methodologies.
  • Further systematic reviews are needed to guide fundamental and applied research in bacterial evolution and adaptation.