CrisPam

CrisPam identifies SNP-derived protospacer adjacent motifs (PAMs) to enable allele-specific targeting by CRISPR/Cas systems for selective editing of variant alleles.

Key Features:

• SNP-derived PAM identification: Detects protospacer adjacent motifs (PAMs) that are generated specifically by single-nucleotide polymorphisms (SNPs).
• Sequence and variant analysis: Analyzes a provided DNA sequence together with reported variations to locate PAM sequences produced by SNPs.
• PAM scanning per report: Scans each reported PAM within a DNA sequence and its variations, ensuring that at least one PAM is generated by an SNP.
• Allele-specificity assessment: Determines whether identified PAMs are exclusive to the variant allele, enabling Cas proteins to target only the variant allele.
• CrisPamDB: Contains analyses of reported pathogenic SNPs in humans and associated SNP-derived PAMs.

Scientific Applications:

• Allele-specific CRISPR therapies: Enables design of CRISPR/Cas strategies that selectively edit mutant alleles in heterozygous patients.
• Reduction of wildtype editing: Increases specificity by selecting PAMs exclusive to variant alleles to minimize editing of wildtype alleles.
• Pathogenic SNP exploration: Supports investigation and application of SNP-derived PAMs for reported pathogenic SNPs in humans via CrisPamDB.

Methodology:

Scans reported PAMs across a provided DNA sequence and its variations to detect PAMs generated by single-nucleotide polymorphisms (SNPs) and identifies PAMs exclusive to variant alleles.