Department of Chemistry, Hanyang University, Seoul, South Korea.
Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany.
BMC Bioinformatics. 2018 Dec 27;19(1):542. doi: 10.1186/s12859-018-2585-4.
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.
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.
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.
由于其简单高效，CRISPR-Cas 系统已被广泛用作基因组编辑工具。最近，开发了 CRISPR 碱基编辑器，它由失活的 Cas9(dCas9)或 Cas9 切口酶(nCas9)与胞嘧啶或鸟嘌呤脱氨酶相连。碱基编辑工具将非常有助于基因校正，因为它们可以在不引入任何供体 DNA 的情况下产生高度特异性的 DNA 替换，但尚未开发出专门的基于网络的工具来方便此类工具的使用。
我们提出了两种碱基编辑器的网络工具，分别命名为 BE-Designer 和 BE-Analyzer。BE-Designer 提供了在给定输入 DNA 序列中所有可能的碱基编辑器目标序列，并提供了包括潜在脱靶位点在内的有用信息。BE-Analyzer 是一种用于从下一代测序(NGS)数据评估碱基编辑结果的工具，它在表格和交互式图形中提供了有关突变的信息。此外，由于该工具在客户端运行，因此不需要将大量靶向深度测序数据(<1GB)上传到服务器，从而大大缩短了运行时间并提高了数据安全性。BE-Designer 和 BE-Analyzer 可分别在 http://www.rgenome.net/be-designer/ 和 http://www.rgenome.net/be-analyzer/ 免费访问。
我们开发了两种有用的网络工具，用于设计目标序列(BE-Designer)和分析 CRISPR 碱基编辑器实验结果的 NGS 数据(BE-Analyzer)。
