Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Dec 13;38(24):5437-5439.
doi: 10.1093/bioinformatics/btac697.

CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design

Christian Anthon  1 , Giulia Ilaria Corsi  1 , Jan Gorodkin  1
Affiliations

CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design

Christian Anthon et al. Bioinformatics. .

Abstract

Summary: The effectiveness of CRISPR/Cas9-mediated genome editing experiments largely depends on the guide RNA (gRNA) used by the CRISPR/Cas9 system for target recognition and cleavage activation. Careful design is necessary to select a gRNA with high editing efficiency at the on-target site and with minimum off-target potential. Here, we present our webserver for gRNA design with a user-friendly graphical interface, which provides interoperability between our on- and off-target prediction tools, CRISPRon and CRISPRoff, for a complete and streamlined gRNA selection.

Availability and implementation: The graphical interface uses the Integrative Genomic Viewer (IGV) JavaScript plugin. The backend tools are implemented in Python and C. The CRISPRon and CRISPRoff webservers and command-line tools are freely available at https://rth.dk/resources/crispr.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Design of gRNAs for Cas9 experiments with CRISPRon/off. Sequence of steps to identify targets that can be edited by Cas9 with high efficiency and with minimum off-target potential. The genomic sequence reported in the table rows is that of the DNA target (5′–3′ strand) which has the same sequence as the gRNA (which binds to the complimentary DNA) and the PAM. The ‘efficiency’ is the predicted indel frequency. The ‘specificity’ is the log10-scaled probability of binding at the on-target site compared to binding anywhere in the genome. The ‘genome’ coordinate is the start position of the target followed by the strand; all targets are in the same region and the same chromosome, which is not shown. IGV, integrative genomic viewer; CDS, coding sequence; 5p-UTR, 5′ untranslated region
See this image and copyright information in PMC

References

    1. Alkan F. et al. (2018) CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters. Genome Biol., 19, 177. - PMC - PubMed
    1. Alkan F. et al. (2017) RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets. Nucleic Acids Res., 45, e60. - PMC - PubMed
    1. Anders C. et al. (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature, 513, 569–573. - PMC - PubMed
    1. Concordet J.-P., Haeussler M. (2018) CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res., 46, W242–W245. - PMC - PubMed
    1. Corsi G.I. et al. (2022) CRISPRroots: on- and off-target assessment of RNA-seq data in CRISPR–Cas9 edited cells. Nucleic Acids Res., 50, e20. - PMC - PubMed

Publication types

MeSH terms

Substances