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

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 userfriendly 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.