JACKIE

JACKIE enumerates genome-wide SpCas9 binding sites to enable design of single-copy and multi-copy CRISPR target sequences and to assess potential off-targets for genome editing and genomic imaging.

Key Features:

• Comprehensive Enumeration: JACKIE enumerates all possible SpCas9 binding sequences across a genome and reports copy number and genomic coordinates.
• Genome-Scale Design Integration: JACKIE supports genome-scale designs by providing genome-wide target sets that can be incorporated into larger experimental frameworks.
• Off-Target Analysis: JACKIE implements fast algorithms to assess sequence neighborhoods of targeting sequences for potential off-target sites.
• Design for Genomic Imaging: JACKIE identifies CRISPR site clusters suitable for genomic imaging applications.

Scientific Applications:

• Genome Editing: Enables selection of SpCas9 target sites with copy-number information and off-target assessment for precise genome editing.
• Epigenome Modification: Provides genome-wide target site enumeration useful for designing CRISPR-based epigenetic perturbations.
• Genomic Imaging: Facilitates design of CRISPR site clusters to visualize and analyze genomic loci.

Methodology:

JACKIE scans genomic sequences to enumerate potential SpCas9 binding sites, evaluates their copy number and spatial distribution, and applies fast algorithms to assess sequence neighborhoods for off-target analysis.