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Computational Tools and Resources for CRISPR/Cas Genome Editing

Genomics, Proteomics & Bioinformatics 2023年第1期21卷 108-126页

作者： Chao Li Wen Chu Rafaqat Ali Gill Shifei Sang Yuqin Shi Xuezhi Hu Yuting Yang Qamar U.Zaman Baohong Zhang Oil Crops Research Institute Chinese Academy of Agricultural SciencesKey Laboratory for Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062China Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081China Department of Biology East Carolina UniversityGreenvilleNC 27858USA

The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)nucleases and their functional variants,as well as in developing precise CRISPR/Cas-derived genome editors.The programmable and robust features of the genome editors provide an effective RNAguided platform for fundamental life science research and subsequent applications in diverse scenarios,including biomedical innovation and targeted crop improvement.One of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts,which strongly depends on the efficiency and specificity of single guide RNA(sgRNA)-directed recognition of targeted DNA sequences.Recent advances in empirical scoring algorithms and machine learning models have facilitated sgRNA design and off-target prediction.In this review,we first briefly introduce the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific purposes.Secondly,we focus on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on-and off-target mutations.Thirdly,we provide insights into the limitations of available computational tools that would help researchers of this field for further optimization.Lastly,we suggest a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.

关键词： Genome editing efficiency and specificity CRISPR/Cas9 sgRNA Computational tool Algorithm

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