发表状态 | 已发表Published |
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
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ISSN/eISSN | 1673-8527 |
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 |
DOI | 10.1016/j.jgg.2024.10.014 |
URL | 查看来源 |
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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