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Data Comparison and Software Design for Easy Selection and Application of CRISPR-based genome Editing Systems in Plants

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genomics, Proteomics & Bioinformatics 2021年第6期19卷 937-948页

作者： Yi Wang Fatma Lecourieux Rui Zhang Zhanwu Dai David Lecourieux Shaohua Li Zhenchang Liang Beijing Key Laboratory of grape Science and Enology and CAS Key Laboratory of Plant ResourcesInstitute of Botanythe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China Ecophysiology and Functional genomics of Vine Bordeaux Sciences AgroINRAEUniversity of BordeauxInstitute of Vine and Wine Sciences Bordeaux-AquitaineVillenave d’Ornon 33140France College of Plant Protection Shandong Agricultural UniversityTaian 271018China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China

CRISPR-based genome editing systems have been successfully and effectively used in many ***,only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome *** many web-based toolkits are available,there is still a shortage of comprehensive,user-friendly,and plant-specific CRISPR databases and desktop *** this study,we identified and analyzed the similarities and differences between CRISPR/Cas9 and CRISPR/Cpf1 systems by considering the abundance of proto-spacer adjacent motif(PAM)sites,the effects of gC content,optimal proto-spacer length,potential universality within the plant kingdom,PAM-rich region(PARR)inhibiting ratio,and the effects of g-quadruplex(g-q)*** this information,we built a comprehensive CRISPR database(including 138 plant genome data sources,***/pc/***),which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 *** also developed a desktop software on the basis of the Perl/Tk tool,which facilitates and improves the detection and analysis of CRISPR editing sites at the whole-genome level on Linux and/or Windows ***,this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.

关键词： CRISPR/Cas PAM-rich region g-q Software Database

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