F. Vasquez Castro, L. D. Sanchez Solis, S. A. Myers
Introduces PrEditR, an open-source, protein-centric tool for high throughput sgRNA design for custom base editor screens, enabling users to designate specific amino acid residues and annotate resulting amino acid changes. Designed for CRISPR-mediated phenotypic screens using base editors and integrates seamlessly with mass-spectrometry-based proteomics experimental outputs. Available on GitHub and Docker Hub.
Motivation: Post-translational modifications (PTMs) are critical to protein activity, yet the biological role of most known modification sites remains uncharacterized. CRISPR-mediated phenotypic screens using base editors offer a powerful approach to dissecting PTM function at scale. However, existing sgRNA design tools for base editing applications are DNA-centric and lack the throughput required to integrate seamlessly with mass-spectrometry-based proteomics experimental outputs. Results: We introduce protein editing in R, PrEditR, an open-source, protein-centric tool for high throughput sgRNA design for custom base editor screens. PrEditR enables users to designate specific amino acid residues in proteins and design protospacer sequences that target the corresponding gene and annotate every resulting amino acid change (missense, nonsense, or silent), including bystander edits. Availability and Implementation: PrEditR is available on GitHub and Docker Hub.