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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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Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I,...
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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints.

Shi Cen1, David A Rasmussen1,2

  • 1Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.

Molecular Biology and Evolution
|June 25, 2024
PubMed
Summary

Recombination detection methods vary in accuracy for locating breakpoints. The number of informative sites is key for accurate breakpoint mapping, improving phylogenetic reconstructions.

Keywords:
ancestral recombination graphbreakpoint localizationinformative sitesphylogeny reconstructionrecombination detection

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Phylogenetic methods reconstruct evolutionary relationships but are hindered by recombination.
  • Recombination obscures ancestral inheritance, necessitating breakpoint detection and alignment selection.

Purpose of the Study:

  • To evaluate the accuracy of recombination detection methods in locating breakpoints.
  • To identify factors influencing breakpoint detection accuracy.

Main Methods:

  • Simulated genome sequences using ancestral recombination graphs.
  • Assessed accuracy of MaxChi, 3SEQ, and Genetic Algorithm Recombination Detection for breakpoint location.

Main Results:

  • Informative sites significantly impact breakpoint detection accuracy.
  • Partitioning alignments using detected breakpoints reduces phylogenetic error.
  • Breakpoint selection strategy has minimal impact on phylogenetic reconstruction quality.

Conclusions:

  • Genomic features, especially informative sites, affect recombination detection performance.
  • Best practices for phylogenetics involve using recombination-free alignments derived from accurate breakpoint detection.