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Related Concept Videos

CRISPR and crRNAs02:53

CRISPR and crRNAs

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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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Genetic Screens02:46

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
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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/Cas9 Genome Editing01:28

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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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CRISPR01:59

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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Related Experiment Video

Updated: Feb 17, 2026

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
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Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

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Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction.

Tyler S Browne1, David R Edgell1, Gregory B Gloor1

  • 1Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada.

Peerj
|February 16, 2026
PubMed
Summary
This summary is machine-generated.

Optimizing data input for CRISPR-Cas9 (CRISPR-associated protein 9) models improves prediction accuracy for antimicrobial applications. This data-centric approach enhances the utility of Cas9 prediction models across bacterial species.

Keywords:
Bacterial CRISPR predictionCRISPR modelCRISPR predictionData cleaningHigh throughput sequencingMachine learningModel buildingSgRNA activity prediction

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Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution
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Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms
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Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms

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Last Updated: Feb 17, 2026

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Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution
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Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms
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Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetic Engineering

Background:

  • The Cas9 enzyme and single-guide RNA (sgRNA) are key tools in genetic engineering, showing potential as species-specific antimicrobials.
  • Accurate prediction of on-target Cas9 cleavage is crucial for its antimicrobial efficacy, as activity varies significantly between targets.
  • Previous research focused on novel deep learning architectures to enhance prediction performance.

Purpose of the Study:

  • To investigate the impact of a data-centric approach on improving Cas9 prediction models.
  • To optimize input data utility by adjusting target site adjacent nucleotide sequence length and filtering control read counts.
  • To develop a generalized bacterial SpCas9 prediction model using the crisprHAL architecture.

Main Methods:

  • Explored data-centric strategies, including optimizing input sequence length and data filtering for read counts.
  • Utilized the existing crisprHAL deep learning architecture to develop a new bacterial SpCas9 prediction model (crisprHAL Tev).
  • Rebuilt two prior Escherichia coli Cas9 datasets to assess data quality's impact.

Main Results:

  • The data-centric approach, specifically input optimization and filtering, significantly improved input data utility for Cas9 prediction.
  • The developed crisprHAL Tev model demonstrated generalized performance across related bacterial species and different data types.
  • Rebuilding the E. coli datasets highlighted the critical role of data quality, leading to an improved bacterial eSpCas9 prediction model.

Conclusions:

  • A data-centric approach is vital for enhancing the performance and generalizability of Cas9 prediction models.
  • The crisprHAL Tev model offers improved prediction accuracy for bacterial SpCas9 activity, applicable across species.
  • Data quality is paramount; improved datasets contribute to more robust and reliable predictive models for CRISPR-based antimicrobials.