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CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR‐Cas system
Author(s) -
Yan Meng,
Zhou ShiRong,
Xue HongWei
Publication year - 2015
Publication title -
journal of integrative plant biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.734
H-Index - 83
eISSN - 1744-7909
pISSN - 1672-9072
DOI - 10.1111/jipb.12295
Subject(s) - crispr , primer (cosmetics) , genome editing , computational biology , cas9 , genetics , biology , chromosome , genome , plasmid , gene , computer science , physics , thermodynamics
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.