BES-Designer: A Web Tool to Design Guide RNAs for Base Editing to Simplify Library.

IF 3.9 2区生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY Interdisciplinary Sciences: Computational Life Sciences Pub Date : 2024-10-28 DOI:10.1007/s12539-024-00663-6

Qian Zhou, Qian Gao, Yujia Gao, Youhua Zhang, Yanjun Chen, Min Li, Pengcheng Wei, Zhenyu Yue

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Abstract

CRISPR/Cas base editors offer precise conversion of single nucleotides without inducing double-strand breaks. This technology finds extensive applications in gene therapy, gene function analysis, and other domains. However, a crucial challenge lies in selecting the appropriate guide RNAs (gRNAs) for base editing. Although various gRNAs design tools exist, creating a simplified base-editing library with diverse protospacer adjacent motifs (PAM) sequences for gRNAs screening remains a challenge. We present a user-friendly web tool, BES-Designer ( https://bes-designer.aielab.net ), for gRNAs design based on base editors, aimed at streamlining the creation of a base-editing library. BES-Designer incorporates our proposed rules for target sequence simplification, helping researchers narrow down the scope of biological experiments in the lab. It allows users to design target sequences with various PAMs and editing types simultaneously, and prioritize them in the simplified base-editing library. This tool has been experimentally proven to achieve a 30% simplification efficiency on the base-editing-library.

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BES-Designer：设计用于碱基编辑的引导 RNA 以简化文库的网络工具。

CRISPR/Cas 碱基编辑器可精确转换单个核苷酸，而不会导致双链断裂。这项技术在基因治疗、基因功能分析和其他领域有着广泛的应用。然而，为碱基编辑选择合适的引导 RNA（gRNA）是一项关键挑战。虽然存在各种 gRNAs 设计工具，但创建一个具有多种原间隔邻接基序（PAM）的简化碱基编辑库来筛选 gRNAs 仍然是一项挑战。我们提出了一种用户友好型网络工具 BES-Designer ( https://bes-designer.aielab.net ) ，用于基于碱基编辑器设计 gRNAs，旨在简化碱基编辑库的创建过程。BES-Designer 融合了我们提出的目标序列简化规则，帮助研究人员缩小实验室生物实验的范围。它允许用户同时设计具有各种 PAM 和编辑类型的目标序列，并在简化的碱基编辑库中对其进行优先排序。实验证明，该工具的碱基编辑库简化效率高达 30%。

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来源期刊

Interdisciplinary Sciences: Computational Life Sciences MATHEMATICAL & COMPUTATIONAL BIOLOGY-

CiteScore

8.60

自引率

4.20%

发文量

期刊介绍： Interdisciplinary Sciences--Computational Life Sciences aims to cover the most recent and outstanding developments in interdisciplinary areas of sciences, especially focusing on computational life sciences, an area that is enjoying rapid development at the forefront of scientific research and technology. The journal publishes original papers of significant general interest covering recent research and developments. Articles will be published rapidly by taking full advantage of internet technology for online submission and peer-reviewing of manuscripts, and then by publishing OnlineFirstTM through SpringerLink even before the issue is built or sent to the printer. The editorial board consists of many leading scientists with international reputation, among others, Luc Montagnier (UNESCO, France), Dennis Salahub (University of Calgary, Canada), Weitao Yang (Duke University, USA). Prof. Dongqing Wei at the Shanghai Jiatong University is appointed as the editor-in-chief; he made important contributions in bioinformatics and computational physics and is best known for his ground-breaking works on the theory of ferroelectric liquids. With the help from a team of associate editors and the editorial board, an international journal with sound reputation shall be created.