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Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants
- Source :
- Genomics, Proteomics and Bioinformatics, Genomics, Proteomics and Bioinformatics, Elsevier, In press, ⟨10.1016/j.gpb.2019.05.008⟩
- Publication Year :
- 2021
- Publisher :
- Elsevier BV, 2021.
-
Abstract
- International audience; CRISPR-based genome editing systems have been successfully and effectively used in many organisms. However, only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome applications. Although many web-based toolkits are available, there is still a shortage of comprehensive, user-friendly, and plant-specific CRISPR databases and desktop software. In 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, effects of GC content, optimal proto-spacer length, potential universality within the plant kingdom, PAM-rich region (PARR) inhibiting ratio, and effects of G-quadruplex (G-Q) structures. Using this information, we built a comprehensive CRISPR database (including 138 plant genome data sources, www.grapeworld.cn/pc/index.html), which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 systems. We also developed a desktop software on the basis of 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 platform. Therefore, this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.
- Subjects :
- 0106 biological sciences
Computer science
G-Q
Computational biology
PARRs
01 natural sciences
Biochemistry
Genome
Database
03 medical and health sciences
CRISPR/Cas
Software
Genome editing
Software Design
Genetics
CRISPR
Molecular Biology
030304 developmental biology
computer.programming_language
Gene Editing
0303 health sciences
Cas9
business.industry
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computational Mathematics
Software design
CRISPR-Cas Systems
Perl
business
computer
Genome, Plant
GC-content
010606 plant biology & botany
Subjects
Details
- ISSN :
- 16720229
- Volume :
- 19
- Database :
- OpenAIRE
- Journal :
- Genomics, Proteomics & Bioinformatics
- Accession number :
- edsair.doi.dedup.....ec8486c13f52c8be7ce2e781a804c1f6
- Full Text :
- https://doi.org/10.1016/j.gpb.2019.05.008