CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

By Tessa G. Montague, J. Cruz, James A. Gagnon, George M. Church, Eivind Valen. Nucleic Acids Res., 2014

1,137 citations recorded by the source corpus.

Major advances in genome editing have recently been made possible with the development of the TALEN and CRISPR/Cas9 methods. The speed and ease of implementing these technologies has led to an explosion of mutant and transgenic organisms. A rate-limiting step in efficiently applying TALEN and CRISPR/Cas9 methods is the selection and design of targeting constructs. We have developed an online tool, CHOPCHOP (https://chopchop.rc.fas.harvard.edu), to expedite the design process. CHOPCHOP accepts a wide range of inputs (gene identifiers, genomic regions or pasted sequences) and provides an array of advanced options for target selection. It uses efficient sequence alignment algorithms to minimize search times, and rigorously predicts off-target binding of single-guide RNAs (sgRNAs) and TALENs. Each query produces an interactive visualization of the gene with candidate target sites displayed at their genomic positions and color-coded according to quality scores. In addition, for each possible target site, restriction sites and primer candidates are visualized, facilitating a streamlined pipeline of mutant generation and validation. The ease-of-use and speed of CHOPCHOP make it a valuable tool for genome engineering.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/538a28e96e7285fa8b474894b37fdfa3dd76665f

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Citations in the corpus

Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites (2015, neutral): “…(Aach et al., 2014; Cradick et al., 2014; Doench et al., 2014; Bae et al., 2014a; Heigwer et al., 2014; Hsu et al., 2013; Lei et al., 2014; Montague et al., 2014; O'Brien and Bailey, 2014; Naito et al., 2014; Sander et al., 2010; Upadhyay and Sharma, 2014; Xie et al., 2014; Zhu et al.,…”
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR (2016, background): “Although published tools and scoring systems allow ranking sequences by specificity [10–22] and efficiency [2, 8, 23–25], they are usually limited to a handful of genomes and only few evidence-based recommendations exist to optimize offtarget search parameters and on-target efficiency.”
Target specificity of the CRISPR-Cas9 system (2014, neutral): “The type of off-targets detected by each tool also varies; most tools only search for off-targets with few (typically three or less) PAM-proximal or total mismatches to the guide [71,75,76,79,80].”
WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system (2015, neutral): “Given the critical roles of gRNA, multiple bioinformatics tools have been developed for rational design of gRNAs for the CRISPR/Cas9 system [14-17].”
Genome Editing—Principles and Applications for Functional Genomics Research and Crop Improvement (2017, background): “off-target effects in genome editing (Lei et al., 2014; Montague et al., 2014; Lee et al., 2016; Rastogi et al., 2016).”
In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency (2015, methodology): “Similarly, CRISPR Design 10 , E-CRISP 14 and CHOPCHOP 15 also use scoring functions with a handful of parameters determined a priori , rather than through a data-driven modeling approach based on principles of statistical estimation, such as we perform herein.”
CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering (2016, background): “CHOP-CHOP (21) provides an intuitive online environment for target selection that optimizes efficiency and specificity according to the latest large-scale studies, as well as performing primer design and restriction site identification, all in a user-friendly, graphical interface (Figure 1).”
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool (2015, background): “To this end, already a number of online sgRNA target finding and evaluation tools like CRISPR Design [13], E-CRISP [16] or CHOPCHOP [17] have been presented.”