Computational Tools and Resources for CRISPR/Cas Genome Editing
文献类型: 外文期刊
第一作者: Li, Chao
作者: Li, Chao;Chu, Wen;Gill, Rafaqat Ali;Sang, Shifei;Shi, Yuqin;Hu, Xuezhi;Yang, Yuting;Zaman, Qamar U.;Chu, Wen;Sang, Shifei;Shi, Yuqin;Yang, Yuting;Zaman, Qamar U.;Zhang, Baohong
作者机构:
关键词: Genome editing; Efficiency and specificity; CRISPR; Cas9; sgRNA; Computational tool; Algorithm
期刊名称:GENOMICS PROTEOMICS & BIOINFORMATICS ( 影响因子:9.5; 五年影响因子:10.1 )
ISSN: 1672-0229
年卷期: 2023 年 21 卷 1 期
页码:
收录情况: SCI
摘要: The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) nucle-ases 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 RNA -guided platform for fundamental life science research and subsequent applications in diverse scenar-ios, 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 scor-ing algorithms and machine learning models have facilitated sgRNA design and off-target predic-tion. 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 limita-tions of available computational tools that would help researchers of this field for further optimiza-tion. Lastly, we suggest a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.
分类号:
- 相关文献
作者其他论文 更多>>
-
Aspartic acid/arginine enhance the stability of gelatin emulsions
作者:Yan, Hui-min;Yao, Xiu-ning;Li, Xue-qing;Xu, Yu-qin;Fang, Shun;Qi, Jun;Xiong, Guo-yuan;Song, Yu;Zhang, Wen-wen;Xu, Ying;Qi, Jun;Li, Chao;Jia, Jing-min;Hu, Yong
关键词:Low-energy emulsification; Thermal stability; Aspartic acid and arginine complexes; Secondary structure; Intermolecular force
-
Growth arrest and DNA damage-inducible 45 ab gene targeted by miR-20b-5p executes the inflammation and apoptosis by regulating MAPK and NF-κB pathways in black rockfish
作者:Gao, Chengbin;Cai, Xin;Zhu, Ying;Cao, Min;Li, Chao;Gao, Chengbin;Cai, Xin;Ma, Le;Sun, Peng
关键词:Ss _ gadd45ab; Inflammation; Apoptosis; Black rockfish; Regulatory mechanism
-
Respiratory mucosal vaccination of peptide-poloxamine-DNA nanoparticles provides complete protection against lethal SARS-CoV-2 challenge
作者:Sun, Si;Zuo, Qianfei;Xu, Chuanfei;Ou, Yangxue;Liu, Chang;Li, Haibo;Li, Chao;Lu, Dongshui;Zhang, Weijun;Luo, Ping;Cheng, Ping;Zou, Quanming;Guan, Shan;Gao, Yuwei;Tu, Changchun;Liu, Yan;Zhao, Gan;Sui, Cheng;Ding, Yuan;Wang, Bin;Tang, Jie;Cai, Larry;Pitard, Bruno;Rosenecker, Joseph;Wang, Bin;Wang, Bin;Liu, Yan;Zou, Quanming;Guan, Shan
关键词:Mucosal vaccine; SARS-CoV-2; DNA vaccine; Pulmonary delivery; Nonviral delivery system
-
Genome-wide association study reveals novel genes on different chromosomal positions regulating boll weight in upland cotton (Gossypium hirsutum L.)
作者:Iqbal, Zubair;Iqbal, Muhammad Shahid;Sarfraz, Zareen;Nazir, Mian Faisal;Hu, Daowu;Zafar, Muhammad Mubashar;Mahmood, Tahir;Pan, Zhaoe;Du, Xiongming;Alamery, Salman;Attia, Kotb;Shehzad, Khurram;Fiaz, Sajid;Zaman, Qamar U.;Zaman, Qamar U.;Attacha, Safira;Zeb, Aqib;Gul, Alia M.;Abushady, Asmaa;Abushady, Asmaa;Kimiko, Itoh A.
关键词:Plant bioinformatics; Genome sequence; Candidate genes; Functional analysis; Yield improvement
-
Optimal Growths from Two Perspectives, with Conditional Macro- and Micro-consistency: Dynamic Summation of Economic Variables Under Differential Regional Representative Production Functions
作者:Yuan, Runze;Xi, Xi;Zhang, Yifan;Liu, Zhentao;Li, Chao;Liang, Yu
关键词:Ramsey model; Equity capital; Risk aversion; Micro-foundations; Multi-regional economic growth
-
Salicylic acid alleviates tidal flooding and salinity toxicity on Barringtonia racemosa seedlings by activating the stress defense mechanism
作者:Xie, Xinquan;Pang, Xinhua;Tan, Xiaohui;Deng, Xu;Hu, Ju;Chen, Wenjia;Yang, Yuting;Liang, Fang;Tan, Xiaohui
关键词:Abiotic stress; Membership function evaluation; Physiology and biochemistry; Secondary metabolism product
-
Genome-wide identification of KNOX transcription factors in cotton and the role of GhKNOX4-A and GhKNOX22-D in response to salt and drought stress
作者:Sun, Runrun;Wang, Yuanyuan;Guo, Xinlei;Sun, Jialiang;Liu, Yongsheng;Wang, Qinglian;Qin, Tengfei;Wall, Sarah Brooke;Zhang, Baohong
关键词:KNOX transcription factor; Drought stress; Oxidative stress; Plant growth; Gene silencing