Web-based design and analysis tools for CRISPR base editing
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Abstract
BACKGROUND: As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed. RESULTS: We present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (< 1 GB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/be-designer/ and http://www.rgenome.net/be-analyzer /, respectively. CONCLUSION: We develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.
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Off-target prediction was performed using CRISPR RGEN Tools allowing up to three mismatches.
“Off-target prediction was done using CRISPR RGEN Tools allowing up to three mismatches in the prediction algorithm [38].”
From Precise CRISPR/Cas9 and Cas12 Correction Using Lipoplexes in Retinal Models Derived from Patients with Inherited Retinal Dystrophies (2026) · cites this paper as [38]
In Implementation > Selection of sgRNAs (page not provided), the paper says BE-Designer uses Cas-OFFinder to predict off-target sequences differing by up to two nucleotides. That contradicts the attributed three-mismatch limit; the passage does not establish what setting the citing authors actually used. (LLM, conf=0.88)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredOff-target prediction was performed using Cas-OFFinder allowing up to three mismatches.
“Off-target prediction was performed using the online tool Cas-OFFinder [38], allowing up to three mismatches.”
From Precise CRISPR/Cas9 and Cas12 Correction Using Lipoplexes in Retinal Models Derived from Patients with Inherited Retinal Dystrophies (2026) · cites this paper as [38]
The Implementation section (‘Selection of sgRNAs’) says BE-Designer uses Cas-OFFinder to search for potential off-target sequences, supporting the tool identification. It specifies sequences differing by up to two nucleotides, not three, so the cited paper does not support the stated mismatch limit. (LLM, conf=0.88)
Experimental — accuracy not yet measured
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- Authors
- Hwang, G.-H., Park, J., Lim, K., Kim, S., Yu, J., Yu, E., Kim, S.-T., Eils, R., Kim, J.-S., & Bae, S.
- Affiliations
- Hanyang University (KR)
- Heidelberg University (DE)
- Seoul National University (KR)
- University Hospital Heidelberg (DE)
- Corresponding author
- Bae, Sangsu
- ORCID
- Venue
- BMC Bioinformatics
- Published
- 2018-12
- Volume
- 19
- Issue
- 1
- Pages
- 542-542
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC6307267
- OpenAlex
- W2883250809
- Cited by
- 198
- References
- 33
- Citations by year
- 2026: 12 · 2025: 34 · 2024: 29 · 2023: 23 · 2022: 27 · 2021: 29 · 2020: 32 · 2019: 12
- FWCI
- 6.49
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- heiDOK (Heidelberg University) (acceptedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- Deutsches Krebsforschungszentrum
- National Research Foundation (2017M3A9G8084539, 2018M3A9H3022412, HI16C1012)
- Ministry of Trade, Industry and Energy (20000158)
- National Research Foundation of Korea (PJ01319301, 2018M3A9H3022412, 20000158, 2017M3A9G8084539)
- 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
- CRISPR base editing, web-based design tool, off-target sites, cytidine deaminase, guanine deaminase, dCas9, next-generation sequencing data analysis, genome editing
- MeSH terms
- Gene Editing, Humans, Internet, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems
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