Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
Harvard School of Engineering and Applied Sciences, Cambridge, MA 02138, USA Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W401-7. doi: 10.1093/nar/gku410. Epub 2014 May 26.
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.
近年来，随着 TALEN 和 CRISPR/Cas9 方法的发展，基因组编辑取得了重大进展。这些技术的实施速度和易用性导致了突变体和转基因生物的爆炸式增长。在有效地应用 TALEN 和 CRISPR/Cas9 方法方面，一个限速步骤是靶向构建体的选择和设计。我们开发了一个在线工具 CHOPCHOP（https://chopchop.rc.fas.harvard.edu），以加快设计过程。CHOPCHOP 接受广泛的输入（基因标识符、基因组区域或粘贴的序列），并提供一系列用于目标选择的高级选项。它使用高效的序列比对算法来最小化搜索时间，并严格预测单指导 RNA（sgRNA）和 TALEN 的脱靶结合。每个查询都会生成一个基因的交互式可视化，候选靶位点显示在其基因组位置，并根据质量分数进行颜色编码。此外，对于每个可能的靶位点，可视化显示限制酶位点和引物候选物，简化了突变体生成和验证的流水线。CHOPCHOP 的易用性和速度使其成为基因组工程的有价值工具。
Zotero 插件