CRIBAR: a fast and flexible sgRNA design tool for CRISPR imaging.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2025-02-12 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbaf022

Xiaoli Chen, Md Mahfuzur Rahaman, Ardalan Naseri, Shaojie Zhang

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引用次数: 0

Abstract

Motivation: CRISPR imaging enables the real-time tracking of nucleic acids. Using guide RNAs (gRNAs) to direct fluorescent tags to target regions allows for precise nucleic acid monitoring via microscopy. The design of gRNAs largely affects the efficacy of CRISPR imaging. Currently, available gRNA design tools are developed primarily for gene editing, often producing individual gRNAs that target genes or regulatory elements.

Results: In this study, we introduce CRIBAR, a computational tool developed to systematically design single-guide RNAs (sgRNAs) for CRISPR imaging applications. CRIBAR first generates sgRNA sets optimized to maximize the number of on-target binding sites and then evaluates the potential off-target effect. The results of the in silico experiment show that CRIBAR enables CRISPR imaging in non-repetitive regions.

Availability and implementation: CRIBAR is available as a software package at https://github.com/ucfcbb/CRIBAR and as a web server at http://genome.ucf.edu/CRIBAR.

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CRIBAR：用于CRISPR成像的快速灵活的sgRNA设计工具。

动机：CRISPR成像可以实现核酸的实时跟踪。使用引导rna （gRNAs）来引导荧光标记到目标区域，可以通过显微镜进行精确的核酸监测。grna的设计在很大程度上影响了CRISPR成像的效果。目前，可用的gRNA设计工具主要用于基因编辑，通常产生针对基因或调控元件的单个gRNA。结果：在本研究中，我们引入了CRIBAR，这是一种用于系统设计用于CRISPR成像应用的单导rna （sgrna）的计算工具。CRIBAR首先生成优化后的sgRNA集，以最大化靶上结合位点的数量，然后评估潜在的脱靶效应。计算机实验结果表明，CRIBAR能够在非重复区域进行CRISPR成像。可用性和实现：CRIBAR作为软件包可在https://github.com/ucfcbb/CRIBAR获得，作为web服务器可在http://genome.ucf.edu/CRIBAR获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量