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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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CRISPR-Cas9 and Its Bioinformatics Tools: A Systematic Review.

Alicja Jasieniecka1, Inês Domingues1,2

  • 1Polytechnic University of Coimbra, Rua da Misericórdia, Lagar dos Cortiços, S. Martinho do Bispo, 3045-093 Coimbra, Portugal.

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Bioinformatics tools are crucial for CRISPR-Cas9 genetic research, aiding in guide RNA design and data analysis. This review highlights the need for integrated, multitasking platforms to streamline complex CRISPR workflows.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Molecular Biology

Background:

  • CRISPR-Cas9 technology has transformed genetic research.
  • Bioinformatics tools are indispensable for CRISPR applications, including guide RNA design, off-target prediction, and data analysis.
  • A systematic review was conducted to assess existing bioinformatics tools for CRISPR-Cas9 research.

Purpose of the Study:

  • To systematically review and summarize the functionality and key features of bioinformatics tools used in CRISPR-Cas9 research.
  • To identify commonly used tools and their primary applications.
  • To highlight limitations and suggest future directions for tool development.

Main Methods:

  • Systematic literature search of PubMed, Google Scholar, and other databases.
  • Inclusion criteria: studies published after 2012.
  • Final search conducted on November 9, 2024.

Main Results:

  • Seven studies met the inclusion criteria, describing approximately 45 bioinformatics tools.
  • Commonly highlighted tools include CRISPResso, CHOPCHOP, and Cas-OFFinder, with a focus on single-guide RNA (sgRNA) design.
  • Most tools addressed specific tasks, often lacked experimental validation, and some exhibited potential author bias.

Conclusions:

  • There is a significant need for integrated, multitasking bioinformatics platforms to simplify CRISPR research workflows.
  • Future tool development should prioritize comprehensive functionality and accessibility.
  • Standardized and experimentally validated platforms are essential for advancing CRISPR-Cas9 research.