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.
Highlights
As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool
CRISPR-mediated base editing tools have been developed. These tools enable the direct conversion of one nucleotide to another without producing DNA double-stranded breaks (DSB) in the target sequence and without the introduction of donor DNA templates
Adenine base editors (ABEs) were constructed by using tRNA adenine deaminase (TadA), evolved to enable the direct conversion of A to G in DNA [16]. Because of their ability to make highly specific DNA substitutions, these base editing tools will be very useful for gene correction [17,18,19,20,21,22], but to the best of our knowledge, a user-friendly and
Summary
As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. We present dedicated web toolkits, named BE-Designer and BE-Analyzer, to aid researchers in choosing sgRNAs to target desired DNA sequences and to assess base editing outcomes from generation sequencing (NGS) data. BE-Designer provides researchers with a list of all possible sgRNAs for targeting given input DNA sequences, along with useful information including their potential off-target sites, for 319 registered organisms, presently.
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