GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes
Abstract
CRISPRi screening has become a powerful approach for functional genomic research. However, the off-target effects resulting from the mismatch tolerance between sgRNAs and their intended targets is a primary concern in CRISPRi applications. To address this issue, we introduce Guide Library Designer (GLiDe), a web-based tool specifically created for the genome-scale design of sgRNA libraries tailored for CRISPRi screening in prokaryotic organisms. GLiDe incorporates a robust quality control framework, rooted in prior experimental knowledge, ensuring the accurate identification of off-target hits. It boasts an extensive built-in database, encompassing 1,397 common prokaryotic species as a comprehensive design resource. In addition, GLiDe provides the capability to design sgRNAs for newly discovered organisms. We further demonstrated that GLiDe exhibits enhanced precision in identifying off-target binding sites for the CRISPRi system.
Copyright and License
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Acknowledgement
We thank Dr. T. Wang (Tsinghua University) for building the original demo of the sgRNA design tool. We also thank members from the C. Zhang and H. Xing laboratories for critical discussions of this work.
Funding
This work was supported by the National Key R&D Program of China [2023YFC3402400 to C.Z.]; the National Natural Science Foundation of China [21938004 to X.X.]; the National Natural Science Foundation of China [U2032210 to C.Z.].
Data Availability
Conflict of Interest
The authors declare that there is no conflict of interest regarding the publication of this article.
Code Availability
Availability and Implementation Freely available on the web at: https://www.thu-big.net/sgRNA_design/.
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Additional details
- 2023YFC3402400
- Ministry of Science and Technology of the People's Republic of China
- 21938004
- National Natural Science Foundation of China
- 21938004
- National Natural Science Foundation of China