Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Cells. 2020 May 22;9(5):1288. doi: 10.3390/cells9051288.
The CRISPR-Cas system has become a cutting-edge technology that revolutionized genome engineering. The use of Cas9 nuclease is currently the method of choice in most tasks requiring a specific DNA modification. The rapid development in the field of CRISPR-Cas is reflected by the constantly expanding ecosystem of computational tools aimed at facilitating experimental design and result analysis. The first group of CRISPR-Cas-related tools that we review is dedicated to aid in guide RNA design by prediction of their efficiency and specificity. The second, relatively new group of tools exploits the observed biases in repair outcomes to predict the results of CRISPR-Cas edits. The third class of tools is developed to assist in the evaluation of the editing outcomes by analysis of the sequencing data. These utilities are accompanied by relevant repositories and databases. Here we present a comprehensive and updated overview of the currently available CRISPR-Cas-related tools, from the perspective of a user who needs a convenient and reliable means to facilitate genome editing experiments at every step, from the guide RNA design to analysis of editing outcomes. Moreover, we discuss the current limitations and challenges that the field must overcome for further improvement in the CRISPR-Cas endeavor.
CRISPR-Cas 系统已成为一项颠覆性技术，彻底改变了基因组工程领域。目前，在大多数需要特定 DNA 修饰的任务中，Cas9 核酸酶的使用是首选方法。CRISPR-Cas 领域的快速发展反映在不断扩展的计算工具生态系统中，这些工具旨在促进实验设计和结果分析。我们回顾的第一组 CRISPR-Cas 相关工具旨在通过预测其效率和特异性来辅助指导 RNA 的设计。第二组相对较新的工具利用观察到的修复结果偏差来预测 CRISPR-Cas 编辑的结果。第三类工具是为了通过分析测序数据来协助评估编辑结果而开发的。这些实用程序伴随着相关的存储库和数据库。在这里，我们从用户的角度全面而更新地介绍了当前可用的 CRISPR-Cas 相关工具，用户需要一种方便可靠的方法来在每个步骤（从指导 RNA 设计到编辑结果分析）促进基因组编辑实验。此外，我们还讨论了该领域必须克服的当前限制和挑战，以进一步改进 CRISPR-Cas 的努力。
