CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

By Kornel Labun, Tessa G. Montague, James A. Gagnon, Summer B. Thyme, Eivind Valen. Nucleic Acids Res., 2016

860 citations recorded by the source corpus.

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

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/11feaf08ffc6feb1f8515c4d00921667c6086353

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Citations in the corpus

DeepCRISPR: optimized CRISPR guide RNA design by deep learning (2018, methodology): “…test data for the four cell lines, respectively, and compared with eight state-of-the-art tools that were trained with human cell line data, including sgRNA Designer [2], SSC [5], CHOP-CHOP [10], CRISPR MultiTargeter [38], E-CRISP [9], sgRNA Scorer [12], Cas-Designer [39], and WU-CRISPR [40] (Fig.”
Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? (2019, background): “…techniques should be considered as ‘gold standards’ for determining gene function and that knockdown approaches, which often result in only a partial LOF, should be used only when null mutants are available for comparison (Schulte-Merker and Stainier, 2014; Lawson, 2016; Stainier et al., 2017).”