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Peer-reviewedCC BYBioinformatics advances

PrEditR: a protein-centric platform for CRISPR-mediated base editor sgRNA design.

  • Felipe Vásquez-Castro1,2
  • Leonardo D Sanchez Solis1
  • Samuel A Myers1,3,4,5
5 affiliations
  1. 1La Jolla Institute for Immunology, Laboratory for Immunochemical Circuits, La Jolla, CA 92037, United States.
  2. 2Bioinformatics and Systems Biology Ph.D. Program, University of California San Diego, La Jolla, CA 92093, United States.
  3. 3Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, United States.
  4. 4Department of Pharmacology, University of California San Diego, La Jolla, CA 92037, United States.
  5. 5Moores Cancer Center, UCSD Health, La Jolla, CA 92037, United States.
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Abstract

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 single-guide RNA (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. 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. PrEditR is available on GitHub and Docker Hub.

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Cite

BibTeXRIS
BibTeX
@article{vasquezcastro2026preditr,
  title = {{PrEditR: a protein-centric platform for CRISPR-mediated base editor sgRNA design.}},
  author = {Felipe Vásquez-Castro and Leonardo D Sanchez Solis and Samuel A Myers},
  journal = {Bioinformatics advances},
  year = {2026},
  month = oct,
  doi = {10.1093/bioadv/vbag323},
  url = {https://europepmc.org/article/MED/42999912},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - PrEditR: a protein-centric platform for CRISPR-mediated base editor sgRNA design.
AU  - Felipe Vásquez-Castro
AU  - Leonardo D Sanchez Solis
AU  - Samuel A Myers
PY  - 2026
DA  - 2026/10/30
JO  - Bioinformatics advances
DO  - 10.1093/bioadv/vbag323
UR  - https://europepmc.org/article/MED/42999912
AB  - 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 single-guide RNA (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. 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. PrEditR is available on GitHub and Docker Hub.
SN  - 2635-0041
ER  -