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pegFinder: A pegRNA designer for CRISPR prime editing

By Ryan D. Chow, Jennifer S. Chen, Johanna Shen, Sidi Chen

Posted 08 May 2020
bioRxiv DOI: 10.1101/2020.05.06.081612

CRISPR technologies have been widely adopted as powerful tools for targeted genomic manipulation. Recently, prime editing, a new CRISPR-based strategy for precision genome editing was developed that enables diverse genomic alterations to be directly written into target sites without requiring double-strand breaks (DSBs) or donor templates. While prime editing is a powerful tool for precision genome editing, the design of its unique prime editing guide RNAs (pegRNAs) is sophisticated for many users. Currently there is no automated tool exists for designing pegRNAs. We therefore developed pegFinder, a standalone algorithm that rapidly designs candidate pegRNAs. This tool enables quick and simple designing and ranking of pegRNAs for virtually any targeted loci simply by entering reference and desired edited sequences. We demonstrated the design with this tool, and showed in a case that among the outputs the top pegRNA recommended by pegFinder is functional in experimental validation. The web portal is available at (http://pegfinder.sidichenlab.org/). pegFinder thus represent the first available online tool for seamless design and recommendation of pegRNAs for diverse prime editing applications. ### Competing Interest Statement The authors have declared no competing interest.

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