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Related Concept Videos

Homologous Recombination02:31

Homologous Recombination

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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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CRISPR and crRNAs02:53

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
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CRISPR Detection From Short Reads Using Partial Overlap Graphs.

Ilan Ben-Bassat1, Benny Chor1

  • 1Blavatnik School of Computer Science, Tel Aviv University , Tel Aviv, Israel .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|April 9, 2016
PubMed
Summary
This summary is machine-generated.

We developed a new method to identify Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) from short DNA reads. This approach improves CRISPR detection, especially when standard genome assembly tools fail.

Keywords:
CRISPR detectionfilteringk-mer countingpartial overlap graphsampling

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are key components of bacterial adaptive immunity and essential tools in gene editing.
  • The increasing volume of microbial sequence data necessitates efficient methods for CRISPR locus identification.
  • Existing automated tools often struggle with repetitive regions in assembled genomes.

Purpose of the Study:

  • To present a novel method for identifying CRISPR repeats directly from raw, short-read sequencing data.
  • To overcome limitations of existing tools that rely on fully assembled genomes.
  • To improve the accuracy and scope of CRISPR detection in diverse microbial species.

Main Methods:

  • Development of an algorithm that identifies CRISPR repeats based on unique sequence characteristics.
  • Utilizes a series of partial overlap graph constructions.
  • Operates directly on raw sequence data, avoiding issues with genome assembly.

Main Results:

  • The method successfully identifies CRISPR repeats in raw sequence data.
  • Demonstrates effectiveness in cases where other tools fail due to assembly challenges.
  • Preliminary implementation shows promising results in detecting CRISPR loci.

Conclusions:

  • The new method offers a robust alternative for CRISPR repeat identification from short reads.
  • It expands the ability to study CRISPR systems in microbes with challenging genomes.
  • This advancement supports broader applications of CRISPR technology in research and biotechnology.