pgRNAFinder

pgRNAFinder predicts and prioritizes paired and single guide RNAs (gRNAs) for CRISPR/Cas genome editing by identifying 3' protospacer-adjacent motifs (PAM), predicting off-target sites, and evaluating deleted-sequence conservation across eight vertebrate genomes.

Key Features:

• 3' PAM-based gRNA search: Identifies candidate gRNAs by searching for the 3' protospacer-adjacent motif (PAM) in input sequences.
• Off-target identification and scoring: Detects possible off-target sites and incorporates them into a scoring system to prioritize high-quality CRISPR sites.
• Deleted-sequence conservation scoring: Evaluates conservation of sequences removed by paired gRNAs and integrates this information into candidate ranking.
• Distance-independent paired-gRNA design: Supports design of distance-independent paired-gRNAs to enable large deletions or insertions.
• Multi-genome support: Performs gRNA design and evaluation across eight vertebrate genomes.

Scientific Applications:

• Precise CRISPR/Cas editing: Enables selection of gRNAs with reduced off-target risk for precise genetic modifications.
• Large genomic deletions and insertions: Facilitates design of paired-gRNAs for generation of large deletions or insertions.
• Functional genomics and disease models: Supports studies of gene function, development of disease models, and exploration of therapeutic interventions via targeted genome edits.

Methodology:

Searches for gRNAs based on the 3' protospacer-adjacent motif (PAM), identifies possible off-target sites, computes scores incorporating off-target predictions and deleted-sequence conservation, applies filtering criteria, and supports analyses across eight vertebrate genomes including distance-independent paired-gRNA design.