CRISPOR

CRISPOR predicts and evaluates CRISPR/Cas9 guide RNA on-target efficiency and off-target effects to support the design of guide RNAs for genome editing experiments.

Key Features:

• Independent evaluation of prediction algorithms: Performs independent evaluation of existing CRISPR/Cas9 prediction algorithms by analyzing data from eight SpCas9 off-target studies to determine reliability and limitations.
• Off-target predictions: Predicts potential off-target sites and identifies most off-targets with mutation rates greater than 0.1% while applying a cutoff on the off-target score to minimize false positives.
• On-target efficiency predictions: Integrates and evaluates multiple on-target efficiency prediction algorithms and reports differences in model performance depending on guide expression context (U6 promoter versus in vitro transcription).
• Comprehensive genome and nuclease support: Supports more than 120 genomes and accommodates different Cas9 proteins for cross-species guide design.
• Efficiency scoring systems: Incorporates and evaluates eight distinct efficiency scoring systems to inform selection of predictive models.

Scientific Applications:

• Guide RNA design for genome editing: Selection and evaluation of guide sequences for CRISPR/Cas9 experiments based on predicted on-target efficiency and off-target risk.
• Off-target assessment in therapeutic contexts: Identification and prioritization of potential off-target sites for applications where precision is critical, such as therapeutic genome editing.
• Comparative evaluation of efficiency models: Comparison of multiple on-target prediction models across expression contexts (U6 promoter versus in vitro transcription) to choose appropriate scoring methods.

Methodology:

Independently evaluates prediction algorithms using data from eight SpCas9 off-target studies; predicts off-targets and applies an off-target score cutoff to detect sites with mutation rates >0.1%; integrates and evaluates multiple on-target efficiency prediction algorithms and eight efficiency scoring systems; supports >120 genomes and various Cas9 proteins.