CRISPRseek

CRISPRseek identifies and scores candidate guide RNAs (gRNAs) for CRISPR-Cas9 systems to maximize on-target activity and minimize off-target cleavage for precise genome editing.

Key Features:

• Flexible gRNA Identification: Identifies potential gRNAs targeting input sequences across various genomes, including support for different bacterial species' CRISPR-Cas9 systems.
• Off-Target Cleavage Scoring: Generates cleavage scores for potential off-target sites using published or user-supplied weight matrices that incorporate position-specific mismatch penalty scores.
• Filtering Options: Filters identified gRNAs based on criteria such as paired orientations or overlap with restriction enzyme sites.
• Discrimination Between Related Sequences: Ranks gRNAs by the difference in predicted cleavage scores between closely related input sequences to aid selection of sequence-specific guides.
• Integration with Bioconductor: Implemented as a Bioconductor package in the R statistical programming environment for integration into computational pipelines.

Scientific Applications:

• RNA-guided nuclease design: Design of target-specific RNA-guided nuclease (CRISPR-Cas9) systems.
• Genetic engineering: Selection of gRNAs for precise genome modifications in genetic engineering experiments.
• Functional genomics: High-throughput gRNA design for functional genomics studies.
• Therapeutic development: Evaluation and selection of gRNAs for therapeutic genome-editing development where specificity is critical.

Methodology:

Uses computational algorithms to analyze input sequences, predict candidate gRNAs, and assess off-target risks using cleavage scoring systems (including published or user-supplied weight matrices with position-specific mismatch penalty scores); implemented in R/Bioconductor.