Cas-Designer

Cas-Designer identifies optimal guide RNA target sites within input DNA sequences for type II CRISPR/Cas-derived RNA-guided endonuclease experiments, evaluating off-target potential and frameshift-inducing likelihood to support gene knockout studies.

Key Features:

• Target enumeration: Generates a comprehensive list of all possible guide RNA target sites within a specified input DNA sequence (e.g., an exon).
• Off-target analysis (mismatches): Identifies potential off-target sites allowing up to 2 nucleotide mismatches.
• Bulge-aware off-target detection: Optionally detects 3 nucleotide bulge-type off-target sites within a chosen genome.
• Out-of-frame scoring: Assigns an "out-of-frame score" to each potential target to estimate the likelihood of producing frameshift mutations for gene knockout.

Scientific Applications:

• Guide selection for gene knockout: Prioritizes target sites predicted to produce frameshift mutations using out-of-frame scores to increase the chance of gene disruption.
• Off-target minimization: Supports selection of candidate guides with reduced unintended editing by evaluating up to 2 mismatches and optional 3 nucleotide bulge-type sites.
• Design for type II CRISPR/Cas experiments: Provides target site choices compatible with type II CRISPR/Cas-derived RNA-guided endonucleases for genome engineering applications.

Methodology:

Enumerates all possible targets from an input DNA sequence, scans a chosen genome for off-target sites allowing up to 2 nucleotide mismatches and optionally 3 nucleotide bulge-type sites, and computes an out-of-frame score for each candidate.