Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
Explore this paper's citation graph
Summary
A novel algorithm termed Cas-OFFinder that searches for potential off-target sites in a given genome or user-defined sequences and allows variations in protospacer-adjacent motif sequences recognized by Cas9, the essential protein component in RGENs.
- Type
- article
- Published
- 2014-01-24
- Cited by
- 2,095
- References
- 17
- Access
- Open access
- OpenAlex
- https://openalex.org/W2115603949
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:6275496
Keywords
CRISPR, Palindrome, Cas9, Biology, Computational biology
References
- RNA-Guided Human Genome Engineering via Cas9
- A TALE nuclease architecture for efficient genome editing
- DNA targeting specificity of RNA-guided Cas9 nucleases
- Enhancing Gene Targeting with Designed Zinc Finger Nucleases
- Indexing Strategies for Rapid Searches of Short Words in Genome Sequences
- A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
- Multiplex Genome Engineering Using CRISPR/Cas Systems
- High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells
- Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
- CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
- Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites
- A library of TAL effector nucleases spanning the human genome
- Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly.
- Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis
- RNA-programmed genome editing in human cells
Cited by
- CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
- Efficient and high-fidelity base editor with expanded PAM compatibility for cytidine dinucleotide
- CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells
- CRISPR/Cas9 editing of the MYO7A gene in rhesus macaque embryos to generate a primate model of Usher syndrome type 1B
- Bioinformatic analysis of RNA from diverse species
- Both TALENs and CRISPR/Cas9 directly target the HBB IVS2–654 (C > T) mutation in β-thalassemia-derived iPSCs
- Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology
- Regulatory RNA-assisted genome engineering in microorganisms.
- The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing.
- Targeted mutagenesis in soybean using the CRISPR-Cas9 system
- Efficient genomic correction methods in human iPS cells using CRISPR-Cas9 system.
- DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins
- How specific is CRISPR/Cas9 really?
- CRISPR Primer Designer: Design primers for knockout and chromosome imaging CRISPR-Cas system.
- Minimizing off-Target Mutagenesis Risks Caused by Programmable Nucleases
- Precision cancer mouse models through genome editing with CRISPR-Cas9
- CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants.
- CRISPR–Cas9-mediated genome editing and guide RNA design
- Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation
- Mouse genome engineering using CRISPR-Cas9 for study of immune function
Related papers
- Engineered CRISPR-Cas9 nucleases with altered PAM specificities
- Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing
- Nanoscale metal-organic frameworks for the intracellular delivery of CRISPR/Cas9 genome editing machinery.
- Editing Aspergillus terreus using the CRISPR-Cas9 system
- Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system
- Increasing the efficiency of CRISPR‐Cas9‐VQR precise genome editing in rice
- CRISPR/Cas9-Based Genome Editing for Disease Modeling and Therapy: Challenges and Opportunities for Nonviral Delivery.
- Improving CRISPR/Cas9-mediated genome editing efficiency in Yarrowia lipolytica using direct tRNA-sgRNA fusions.
- Predicting Off-Target Potential of CRISPR-Cas9 Single Guide RNA