用于全基因组CRISPR设计与优化的CRISPR-DO
CRISPR-DO for genome-wide CRISPR design and optimization.
作者信息
Ma Jian, Köster Johannes, Qin Qian, Hu Shengen, Li Wei, Chen Chenhao, Cao Qingyi, Wang Jinzeng, Mei Shenglin, Liu Qi, Xu Han, Liu Xiaole Shirley
机构信息
School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
出版信息
Bioinformatics. 2016 Nov 1;32(21):3336-3338. doi: 10.1093/bioinformatics/btw476. Epub 2016 Jul 10.
MOTIVATION
Despite the growing popularity in using CRISPR/Cas9 technology for genome editing and gene knockout, its performance still relies on well-designed single guide RNAs (sgRNA). In this study, we propose a web application for the Design and Optimization (CRISPR-DO) of guide sequences that target both coding and non-coding regions in spCas9 CRISPR system across human, mouse, zebrafish, fly and worm genomes. CRISPR-DO uses a computational sequence model to predict sgRNA efficiency, and employs a specificity scoring function to evaluate the potential of off-target effect. It also provides information on functional conservation of target sequences, as well as the overlaps with exons, putative regulatory sequences and single-nucleotide polymorphisms (SNPs). The web application has a user-friendly genome-browser interface to facilitate the selection of the best target DNA sequences for experimental design.
AVAILABILITY AND IMPLEMENTATION
CRISPR-DO is available at http://cistrome.org/crispr/ CONTACT: qiliu@tongji.edu.cn or hanxu@jimmy.harvard.edu or xsliu@jimmy.harvard.eduSupplementary information: Supplementary data are available at Bioinformatics online.
动机
尽管使用CRISPR/Cas9技术进行基因组编辑和基因敲除越来越流行，但其性能仍依赖于精心设计的单向导RNA（sgRNA）。在本研究中，我们提出了一种用于设计和优化（CRISPR-DO）引导序列的网络应用程序，该引导序列靶向人、小鼠、斑马鱼、果蝇和线虫基因组中spCas9 CRISPR系统的编码和非编码区域。CRISPR-DO使用计算序列模型来预测sgRNA效率，并采用特异性评分函数来评估脱靶效应的可能性。它还提供有关靶序列功能保守性的信息，以及与外显子、推定调控序列和单核苷酸多态性（SNP）的重叠信息。该网络应用程序具有用户友好的基因组浏览器界面，便于为实验设计选择最佳靶DNA序列。
可用性和实施
CRISPR-DO可在http://cistrome.org/crispr/获取 联系方式：qiliu@tongji.edu.cn或hanxu@jimmy.harvard.edu或xsliu@jimmy.harvard.edu 补充信息：补充数据可在《生物信息学》在线获取。
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