GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes
Abstract Background 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. Results We introduce Guide Library Desig...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-024-06012-0 |
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| author | Tongjun Xiang Huibao Feng Xin-hui Xing Chong Zhang |
| author_facet | Tongjun Xiang Huibao Feng Xin-hui Xing Chong Zhang |
| author_sort | Tongjun Xiang |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. It also provides the capability to design sgRNAs for newly discovered organisms by accepting uploaded design resource. We further demonstrated that GLiDe exhibits enhanced precision in identifying off-target binding sites for the CRISPRi system. Conclusions We present a web server that allows the construction of genome-scale CRISPRi sgRNA libraries for prokaryotes. It mitigates off-target effects through a robust quality control framework, leveraging prior experimental knowledge within an end-to-end, user-friendly pipeline. |
| format | Article |
| id | doaj-art-866ea52c619545279964719b812b645f |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-866ea52c619545279964719b812b645f2025-01-05T12:48:12ZengBMCBMC Bioinformatics1471-21052025-01-0126111410.1186/s12859-024-06012-0GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotesTongjun Xiang0Huibao Feng1Xin-hui Xing2Chong Zhang3MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua UniversityMOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua UniversityMOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua UniversityMOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua UniversityAbstract Background 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. Results 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. It also provides the capability to design sgRNAs for newly discovered organisms by accepting uploaded design resource. We further demonstrated that GLiDe exhibits enhanced precision in identifying off-target binding sites for the CRISPRi system. Conclusions We present a web server that allows the construction of genome-scale CRISPRi sgRNA libraries for prokaryotes. It mitigates off-target effects through a robust quality control framework, leveraging prior experimental knowledge within an end-to-end, user-friendly pipeline.https://doi.org/10.1186/s12859-024-06012-0CRISPRi sgRNA designOff-target binding identificationPublic webserver |
| spellingShingle | Tongjun Xiang Huibao Feng Xin-hui Xing Chong Zhang GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes BMC Bioinformatics CRISPRi sgRNA design Off-target binding identification Public webserver |
| title | GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes |
| title_full | GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes |
| title_fullStr | GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes |
| title_full_unstemmed | GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes |
| title_short | GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes |
| title_sort | glide a web based genome scale crispri sgrna design tool for prokaryotes |
| topic | CRISPRi sgRNA design Off-target binding identification Public webserver |
| url | https://doi.org/10.1186/s12859-024-06012-0 |
| work_keys_str_mv | AT tongjunxiang glideawebbasedgenomescalecrisprisgrnadesigntoolforprokaryotes AT huibaofeng glideawebbasedgenomescalecrisprisgrnadesigntoolforprokaryotes AT xinhuixing glideawebbasedgenomescalecrisprisgrnadesigntoolforprokaryotes AT chongzhang glideawebbasedgenomescalecrisprisgrnadesigntoolforprokaryotes |