J Integr Plant Biol. ›› 2015, Vol. 57 ›› Issue (7): 613-617.DOI: 10.1111/jipb.12295

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CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system

Meng Yan, Shi-Rong Zhou* and Hong-Wei Xue*   

  1. National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, China


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.


Yan M, Zhou SR, Xue HW (2015) CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system. J Integr Plant Biol 57: 613–617. doi: 10.1111/jipb.12295

Key words: Chromosome imaging, CRISPR, knockout, primer, software

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