CHOPCHOP

CHOPCHOP identifies CRISPR-Cas single guide RNA targets for targeted mutagenesis, RNA targeting, and diverse CRISPR applications across over 200 genomes.

Key Features:

• CRISPR effector support: Supports Cas9, Cas9 nickase, Cas13, Cpf1/CasX, and TALEN-directed mutagenesis.
• RNA targeting with Cas13: Enables precise RNA targeting with support for alternative transcript isoforms and RNA accessibility prediction using ViennaRNA's RNAfold.
• DNA targeting modes: Includes CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes.
• Genome and search capabilities: Supports over 200 genomes with whole-gene targeting and versatile search modes.
• Visualization: Displays results with alternative isoforms and downstream ATG sites to aid in avoiding truncated protein expression.
• Command-line version: Available for larger queries and handling unsupported genomes with additional functionalities.
• Off-target prediction: Rigorously predicts off-target binding of sgRNAs and TALENs.
• Custom sgRNA length support: Provides support for custom length sgRNAs to increase targeting range and specificity.
• Sequence composition evaluation: Evaluates the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies.
• Restriction sites and primer visualization: Visualizes restriction sites and primer candidates for each possible target site.

Scientific Applications:

• Gene knock-out: Designs gRNAs for efficient gene knockout across supported genomes.
• RNA knock-down: Designs gRNAs for targeted RNA degradation using Cas13.
• Sequence knock-in: Designs gRNAs for knock-in applications using homologous recombination or non-homologous end joining.
• dCas9 fusion/effector targeting: Designs gRNAs for CRISPR activation and repression applications.
• Targeted enrichment for long-read sequencing: Enriches loci for long-read sequencing applications.
• Cas9 repair outcome prediction: Predicts repair outcomes following Cas9-induced DNA cleavage.
• Transgenic or plasmid sequence targeting: Designs gRNAs for targeting transgenic or plasmid sequences.
• Cas9 nickase applications: Designs gRNAs for knock-in using Cas9 nickases.

Methodology:

CHOPCHOP uses efficient sequence alignment algorithms to minimize search times and evaluates sgRNA sequence composition using models compiled from multiple large-scale studies. RNA accessibility predictions employ ViennaRNA's RNAfold.