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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W401-7. doi: 10.1093/nar/gku410. Epub 2014 May 26.

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

Author information

1
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
2
Harvard School of Engineering and Applied Sciences, Cambridge, MA 02138, USA Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA.
3
Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
4
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA eivind.valen@gmail.com.

Abstract

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.

PMID:
24861617
PMCID:
PMC4086086
DOI:
10.1093/nar/gku410
[Indexed for MEDLINE]
Free PMC Article
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