title: CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system.
abstract: The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system.
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Yan
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Shi-Rong
authors.initials: SR
authors.lastname: Zhou
authors.affiliation: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Xue
mesh_terms: D064113:CRISPR-Cas Systems / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D017931:DNA Primers / Q000378:metabolism*; D055786:Gene Knockout Techniques; D021621:Imaging, Three-Dimensional; D012984:Software
chemical_list: D017931:DNA Primers
keywords: CRISPR; Chromosome imaging; knockout; primer; software