Web-based design and analysis tools for CRISPR base editing

• DOI: 10.1186/s12859-018-2585-4
• Publication Date: 2018-12-26T19:29:48Z
• Authors: Gue-Ho Hwang; Jeongbin Park; Kayeong Lim; Sunghyun Kim; Jihyeon Yu; Eunchong Yu; Sang-Tae Kim; Roland Eils; Jin-Soo Kim; Sangsu Bae
• Keywords: Gene Editing; 0301 basic medicine; 570; Internet; QH301-705.5; NGS analysis; Computer applications to medicine. Medical informatics; R858-859.7; 610; 570 Life sciences; Base editing; 03 medical and health sciences; 610 Medical sciences Medicine; CRISPR; Humans; Clustered Regularly Interspaced Short Palindromic Repeats; Web-based tool; Biology (General); CRISPR-Cas Systems; Software; Genome editing

AbstractBackgroundAs 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 (>100MB) 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/bedesigner/ and http://www.rgenome.net/be-analyzer/respectivelyConclusionWe 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.