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DOE OSTI · 3014545

CRISPR-COPIES: Web Tool

Boob, Aashutosh Girish·Jain, Manan·Petrov, Vassily Andrew·Zhao, Huimin
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Abstract

CRISPR/Cas system has emerged as a powerful genome-editing tool for metabolic engineering and human gene therapy. However, the conundrum of where to integrate heterologous genes on the chromosome using the CRISPR/Cas system remains an open question. Selecting a site for gene integration requires incorporation of complex criteria such as factors involved in CRISPR/Cas-mediated integration, genetic stability, and gene expression and therefore, usually requires strenuous characterization of sites on particular or different chromosomal locations. To address these issues, we developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. The tool applies ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. This submission contains the code we developed to create a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate CRISPR-COPIES will serve as a useful tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.

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BioinformaticsCRISPRFOS: Computer and information sciencesIntegration SitesMetabolic EngineeringSynthetic Biology

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Boob, Aashutosh Girish, Jain, Manan, Petrov, Vassily Andrew, Zhao, Huimin. 2023-09-06. CRISPR-COPIES: Web Tool. https://doi.org/10.5281/zenodo.7980074

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