CRISPR-COPIES: An In silico Platform for Discovery of Neutral Integration Sites for CRISPR/Cas-facilitated Gene Integration

Themes: Conversion

Keywords: Software


Boob, A.G., Jain, M., Petrov, V.A.,  Zhao, H. Sept. 6, 2023. “CRISPR-COPIES: Web Tool.” Zenodo. DOI: 10.5281/zenodo.10519505.


Overview and application of CRISPR-COPIES in the field of biotechnology.

COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites (CRISPR-COPIES) is a user-friendly web application and a command line tool for rapid discovery of neutral integration sites. Designed to work for any organism with a genome in NCBI and for any CRISPR system, CRISPR-COPIES can identify neutral sites in a genome-wide manner. The identified sites can be used for characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.


GitHub Repository: Includes code, essential genes, and experimental validation

Zenodo: Includes software

Web application

Download (6.8 MB) includes:

  • Primers
  • Integration sites
  • Plasmids/strains

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