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Conservative Site-specific Recombination and Phase Variation02:53

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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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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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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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Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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A new method for modeling coalescent processes with recombination.

Ying Wang, Ying Zhou, Linfeng Li

  • 1Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China. mazm@amt.ac.cn.

BMC Bioinformatics
|August 13, 2014
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Summary
This summary is machine-generated.

A new Spatial Coalescent simulator (SC) models recombination and coalescence, improving ancestral recombination graph (ARG) generation. This method simplifies evolutionary parameter estimation and reduces computational burden in population genomics.

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Area of Science:

  • Population genomics
  • Evolutionary biology
  • Computational biology

Background:

  • Recombination is crucial for genetic diversity in eukaryotes but complicates evolutionary parameter estimation.
  • Ancestral Recombination Graphs (ARGs) model recombination, with existing methods like ms (back-in-time) and Wiuf&Hein's (spatial) having limitations.
  • Approximate methods like SMC, SMC', and MaCS are also used for ARG simulation.

Purpose of the Study:

  • To develop a novel method for modeling coalescence with recombination.
  • To improve upon existing algorithms for simulating Ancestral Recombination Graphs (ARGs).
  • To provide a more computationally efficient approach for analyzing genetic data.

Main Methods:

  • Developed a new Spatial Coalescent simulator (SC) algorithm.
  • Constructed ARGs spatially along the sequence, avoiding redundant branches.
  • Demonstrated the equivalence of SC's ARG distribution to the back-in-time model (ms).

Main Results:

  • The SC algorithm generates ARGs without redundant branches, unlike the Wiuf&Hein algorithm.
  • ARG distributions from SC are identical to the ms model.
  • SC's TMRCA estimates are closer to ms than MaCS, and it can generate sample-consistent ARGs.
  • Existing methods (SMC, SMC', MaCS) are shown to be special cases of the SC method.

Conclusions:

  • The new SC method and algorithm facilitate the estimation and description of recombination.
  • This approach offers potential for reduced computational burden in population genomics and evolutionary studies.
  • The findings may advance our understanding of genetic diversity and disease mapping.