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CHOPCHOP v2: A Web Tool for the Next Generation of CRISPR Genome Engineering

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CHOPCHOP v2: A Web Tool for the Next Generation of CRISPR Genome Engineering

Kornel Labun et al. Nucleic Acids Res.

Abstract

In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no.

Figures

Figure 1.
Figure 1.
The workflow of CHOPCHOP in Cas9 nickase mode. The CHOPCHOP homepage (upper box) allows three types of input (DNA sequence, genomic coordinates or gene IDs) with default parameters optimized for novice users. For experienced users, a number of options for Cas9, Cas9 nickase, Cpf1 and TALEN mode can be revealed. The results of the search (middle box) are displayed across the gene, genomic region or DNA sequence, depending on the input format. The target color indicates the quality of each sgRNA or nickase pair (green [best] to red [worst]). The graphic representation of the search area is complemented by an interactive table below (not shown). Each sgRNA or nickase pair can be explored in greater detail (lower box) with annotated primer candidates and restriction sites, and information about any off-targets (not shown). Nickases are displayed in red and blue with the intermediate region in black.
Figure 2.
Figure 2.
CHOPCHOP results can be exported to the UCSC browser with a single click. Here, the sgRNAs (in this example in promoter-targeting mode) are viewed in the context of the genome. The tracks displayed in this example are DNase sensitive regions, common SNPs and CpG islands.

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