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题名PAMPHLET: PAM Prediction HomoLogous-Enhancement Toolkit for precise PAM prediction in CRISPR-Cas systems
作者
发表日期2025-02-01
发表期刊Journal of Genetics and Genomics
ISSN/eISSN1673-8527
卷号52期号:2页码:258-268
摘要

CRISPR-Cas technology has revolutionized our ability to understand and engineer organisms, evolving from a singular Cas9 model to a diverse CRISPR toolbox. A critical bottleneck in developing new Cas proteins is identifying protospacer adjacent motif (PAM) sequences. Due to the limitations of experimental methods, bioinformatics approaches have become essential. However, existing PAM prediction programs are limited by the small number of spacers in CRISPR-Cas systems, resulting in low accuracy. To address this, we develop PAMPHLET, a pipeline that uses homology searches to identify additional spacers, significantly increasing the number of spacers up to 18-fold. PAMPHLET is validated on 20 CRISPR-Cas systems and successfully predicts PAM sequences for 18 protospacers. These predictions are further validated using the DocMF platform, which characterizes protein–DNA recognition patterns via next-generation sequencing. The high consistency between PAMPHLET predictions and DocMF results for Cas proteins demonstrates the potential of PAMPHLET to enhance PAM sequence prediction accuracy, expedite the discovery process, and accelerate the development of CRISPR tools.

关键词Computational framework CRISPR-Cas Genome editing PAM prediction Protospacer adjacent motif
DOI10.1016/j.jgg.2024.10.014
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语种英语English
Scopus入藏号2-s2.0-85212655922
引用统计
文献类型期刊论文
条目标识符https://repository.uic.edu.cn/handle/39GCC9TT/12518
专题理工科技学院
通讯作者Wang, Dan
作者单位
1.Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science,BNU-HKBU United International College,Zhuhai,Guangdong,519087,China
2.School of Biology and Biological Engineering,South China University of Technology,Guangzhou,Guangdong,510006,China
3.BGI Research,Hangzhou,Zhejiang,310030,China
4.BGI Research,Shenzhen,Guangdong,518083,China
5.College of Life Sciences,University of Chinese Academy of Sciences,Beijing,100049,China
6.Laboratory of Integrative Biomedicine,Department of Biology,Faculty of Science,University of Copenhagen,Copenhagen,Denmark
7.Qingdao-Europe Advanced Institute for Life Sciences,BGI Research,Qingdao,Shandong,266555,China
8.School of Life Science,Hangzhou Institute for Advanced Study,University of Chinese Academy of Sciences,Hangzhou,Zhejiang,310024,China
9.STOmics Americas Ltd.,San Jose,2904 Orchard Pkwy,95134,United States
第一作者单位北师香港浸会大学
通讯作者单位北师香港浸会大学
推荐引用方式
GB/T 7714
Qi, Chen,Shen, Xuechun,Li, Baitaoet al. PAMPHLET: PAM Prediction HomoLogous-Enhancement Toolkit for precise PAM prediction in CRISPR-Cas systems[J]. Journal of Genetics and Genomics, 2025, 52(2): 258-268.
APA Qi, Chen., Shen, Xuechun., Li, Baitao., Liu, Chuan., Huang, Lei., .. & Wang, Dan. (2025). PAMPHLET: PAM Prediction HomoLogous-Enhancement Toolkit for precise PAM prediction in CRISPR-Cas systems. Journal of Genetics and Genomics, 52(2), 258-268.
MLA Qi, Chen,et al."PAMPHLET: PAM Prediction HomoLogous-Enhancement Toolkit for precise PAM prediction in CRISPR-Cas systems". Journal of Genetics and Genomics 52.2(2025): 258-268.
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