Web-based design and analysis tools for CRISPR base editing |
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Authors: | Gue-Ho Hwang Jeongbin Park Kayeong Lim Sunghyun Kim Jihyeon Yu Eunchong Yu Sang-Tae Kim Roland Eils Jin-Soo Kim Sangsu Bae |
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Institution: | 1.Department of Chemistry,Hanyang University,Seoul,South Korea;2.Center for Digital Health, Berlin Institute of Health and Charité Universit?tsmedizin Berlin,Berlin,Germany;3.Faculty of Biosciences, Heidelberg University,Heidelberg,Germany;4.Department of Chemistry,Seoul National University,Seoul,South Korea;5.Center for Genome Engineering,Institute for Basic Science,Seoul,South Korea;6.Research Institute for Convergence of Basic Sciences,Hanyang University,Seoul,South Korea;7.Center for Genome Engineering, Institute for Basic Science,Daejeon,South Korea;8.Health Data Science Unit, Heidelberg University Hospital,Heidelberg,Germany |
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Abstract: | BackgroundAs 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.ResultsWe 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. ConclusionWe 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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