CRISpy-pop

CRISpy-pop generates and filters CRISPR/Cas9 guide RNA sequences using population genomic data to design guides across diverse Saccharomyces cerevisiae and Zymomonas mobilis strains for multi-strain genome editing.

Key Features:

• gRNA generation and filtration: Produces and filters candidate CRISPR/Cas9 guide RNA sequences tailored to target loci across genomes.
• Multi-strain design capability: Supports design across over 1000 Saccharomyces cerevisiae genomes, including 167 bioenergy-relevant strains, and extends to Zymomonas mobilis.
• Human genome cross-referencing: Compares candidate gRNAs against the human genome to identify and flag potential off-targets for biosafety assessment.
• Strain coverage prediction: Predicts the coverage of each designed guide RNA across the supported strain sets to assess multi-strain targeting breadth.
• Validation of activity prediction: Validated to predict gRNA activity across different strains using population genomic data.

Scientific Applications:

• Bioenergy strain engineering: Design and select gRNAs for genome editing of Saccharomyces cerevisiae and Zymomonas mobilis strains to modify metabolic pathways for biofuel production.
• Functional population genetics: Enable functional population genetic studies by identifying guides with predicted activity and coverage across multiple strains.

Methodology:

Generation and filtration of CRISPR/Cas9 guide RNA sequences; leveraging population genomic data from >1000 S. cerevisiae genomes and Zymomonas mobilis; cross-referencing gRNAs against the human genome; predicting guide coverage across supported strain sets; validation of gRNA activity predictions using population genomic data.