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*   

  • 收稿日期:2014-08-10 接受日期:2014-10-08 出版日期:2014-10-16 发布日期:2014-10-16

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

被引次数

28

摘要： CRISPR Primer Designer helps CRISPR-Cas system users to choose specific spacer sequences for genomes editing and chromosome imaging. Not only for plants, but for all organisms that support Whole Genome BLAST in NCBI, local BLAST or other sites. We will update the program continually.

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.

 

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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