CasOT: A genome-wide cas9/gRNA off-target searching tool
Abstract
The CRISPR/Cas or Cas9/guide RNA system is a newly developed, easily engineered and highly effective tool for gene targeting; it has considerable off-target effects in cultured human cells and in several organisms. However, the Cas9/guide RNA target site is too short for existing alignment tools to exhaustively and effectively identify potential off-target sites. CasOT is a local tool designed to find potential off-target sites in any given genome or user-provided sequence, with user-specified types of protospacer adjacent motif, and number of mismatches allowed in the seed and non-seed regions. AVAILABILITY: http://eendb.zfgenetics.org/casot/ CONTACT: zfgenetics@gmail.com or bzhang@pku.edu.cn Supplementary Information: Supplementary data are available at Bioinformatics online.
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CasOT is the first exhaustive tool to predict off-target sites in a user-provided reference genome, and it allows custom adjustment of the PAM sequence and the mismatch number.
“CasOT is the first exhaustive tool to predict off-target sites in user-provided reference genome, and it allows custom adjustment of several parameters including the PAM sequence and the mismatch number (Xiao et al., 2014).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Xiao et al., 2014
AAV delivery in vivo lasts for years in terminally differentiated cell types.
“| Delivery methods improvement | Application in vivo [95–105] | AAV: Last for years in terminally differentiated cell types | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [95]
LNP delivery in vivo can be quickly degraded.
“| Delivery methods improvement | Application in vivo [95–105] | LNP: Can be quickly degraded in vivo | Eliminate off-target effects |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [95]
AAV delivery in vivo may cause accumulation of off-target mutations.
“| Delivery methods improvement | Application in vivo [95–105] | AAV: Last for years in terminally differentiated cell types | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [95]
LNP delivery in vivo eliminates off-target effects.
“| Delivery methods improvement | Application in vivo [95–105] | LNP: Can be quickly degraded in vivo | Eliminate off-target effects |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [95]
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- Authors
- Xiao, A., Cheng, Z., Kong, L., Zhu, Z., Lin, S., Gao, G., & Zhang, B.
- Affiliations
- University of California, Los Angeles (US)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-01-02
- Volume
- 30
- Issue
- 8
- Pages
- 1180-1182
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2115189270
- Cited by
- 363
- References
- 17
- Citations by year
- 2026: 9 · 2025: 23 · 2024: 31 · 2023: 30 · 2022: 30 · 2021: 30 · 2020: 30 · 2019: 36 · 2018: 30 · 2017: 21 · 2016: 42 · 2015: 24 · 2014: 25
- FWCI
- 15.30
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR-Cas, off-target sites, protospacer adjacent motif, gene targeting
- MeSH terms
- RNA, Guide, CRISPR-Cas Systems, Humans, Software, Gene Targeting, Computational Biology, CRISPR-Cas Systems
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