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Web-based design and analysis tools for CRISPR base editing

Hwang, Gue-Ho ; Park, Jeongbin ; Lim, Kayeong ; Kim, Sunghyun ; Yu, Jihyeon ; Yu, Eunchong ; Kim, Sang-Tae ; Eils, Roland ; Kim, Jin-Soo ; Bae, Sangsu

In: BMC Bioinformatics, 19 (2018), Nr. 542. pp. 1-7. ISSN 1471-2105

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Download (1MB) | Lizenz: Creative Commons LizenzvertragWeb-based design and analysis tools for CRISPR base editing by Hwang, Gue-Ho ; Park, Jeongbin ; Lim, Kayeong ; Kim, Sunghyun ; Yu, Jihyeon ; Yu, Eunchong ; Kim, Sang-Tae ; Eils, Roland ; Kim, Jin-Soo ; Bae, Sangsu underlies the terms of Creative Commons Attribution 4.0

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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.

Item Type: Article
Journal or Publication Title: BMC Bioinformatics
Volume: 19
Number: 542
Publisher: BioMed Central ; Springer
Place of Publication: London ; Berlin ; Heidelberg
Date Deposited: 08 Feb 2019 11:51
Date: 2018
ISSN: 1471-2105
Page Range: pp. 1-7
Faculties / Institutes: Service facilities > Interfakultäre Biomedizinische Forschungseinrichtung (IBF)
Subjects: 570 Life sciences
610 Medical sciences Medicine
Uncontrolled Keywords: CRISPR, Base editing, Web-based tool, Genome editing, NGS analysis
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