Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
Open accessAbstract
SUMMARY: The Type II clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system is an adaptive immune response in prokaryotes, protecting host cells against invading phages or plasmids by cleaving these foreign DNA species in a targeted manner. CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) enable genome editing in cultured cells, animals and plants, but are limited by off-target mutations. Here, we present a novel algorithm termed Cas-OFFinder that searches for potential off-target sites in a given genome or user-defined sequences. Unlike other algorithms currently available for identification of RGEN off-target sites, Cas-OFFinder is not limited by the number of mismatches and allows variations in protospacer-adjacent motif sequences recognized by Cas9, the essential protein component in RGENs. Cas-OFFinder is available as a command-line program or accessible via our website. AVAILABILITY AND IMPLEMENTATION: Cas-OFFinder free access at http://www.rgenome.net/cas-offinder. CONTACT: baesau@snu.ac.kr or jskim01@snu.ac.kr.
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Cas-OFFinder is more widely applicated due to its high tolerance of sgRNA length, PAM types, and the number of mismatches or bulges.
“Cas-OFFinder is more widely applicated due to its high tolerance of sgRNA length, PAM types, and the number of mismatches or bulges (Bae et al., 2014).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Bae et al., 2014
The Results and Discussion section reports searches using 20-bp and 24-bp guide-matching sequences and different PAMs; its conclusion says Cas-OFFinder does not limit the number of mismatched bases. The Methods section describes counting mismatches, but no passage establishes that the tool tolerates bulges. That part of the claim is unsupported by this copy. (LLM, conf=0.87)
Experimental — accuracy not yet measuredPotential sgRNA-specific off-target events were predicted using the Cas-OFFinder open recourse tool.
“Potential sgRNA-specific off-target events were predicted using the Cas-OFFinder open recourse tool76.”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [76]
The off-target analysis found no genomic locations among the predicted CRISPR off-targets that carried variants in the K27M-P T RNA-seq sample but not in the Trp53+/+ controls (EV-ctl and EV-PDGFRA).
“We found that none of the potential off-target genomic locations harbored variants in K27M-P T RNA-seq sample that were not also found in the Trp53+/+ control samples (EV-ctl and EV-PDGFRA).”
From H3.3K27M Cooperates with Trp53 Loss and PDGFRA Gain in Mouse Embryonic Neural Progenitor Cells to Induce Invasive High-Grade Gliomas (2017) · cites this paper as Bae et al., 2014
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“Potential sgRNA-speci fi c off-target events were predicted using the Cas-OFFinder open recourse tool 76 .”
Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors
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- Authors
- Bae, S., Park, J., & Kim, J.-S.
- Affiliations
- Seoul National University (KR)
- Corresponding author
- Bae, Sangsu
- Kim, Jin-Soo
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-01-24
- Volume
- 30
- Issue
- 10
- Pages
- 1473-1475
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4016707
- OpenAlex
- W2115603949
- Cited by
- 2,339
- References
- 17
- Citations by year
- 2026: 229 · 2025: 275 · 2024: 266 · 2023: 296 · 2022: 266 · 2021: 264 · 2020: 224 · 2019: 174 · 2018: 130 · 2017: 79 · 2016: 64 · 2015: 45 · 2014: 25
- FWCI
- 29.09
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- National Research Foundation
- National Research Foundation of Korea
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Cas9, CRISPR/Cas9, RNA-guided nucleases, genome editing, protospacer adjacent motif, mismatch tolerance
- MeSH terms
- CRISPR-Associated Protein 9, Algorithms, Animals, Bacterial Proteins, Base Sequence, DNA, Endonucleases, Humans, Software, Time Factors, Genome, Human, Sequence Analysis, DNA, Genome, Plant, Mice, RNA, Small Untranslated
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