A PLATFORM TO AID SELECT THE OPTIMAL TOOL TO DESIGN GUIDE RNAS

doi:10.15302/J-FASE-2022479

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Qianqian YANG, Lei MA(

)

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China

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Abstract

● Summaries on sgRNAs design.

● Overview of the features of 43 web sgRNA designers.

● A platform to select optimal sgRNA design tool.

CRISPR-mediated gene-editing technology has arguably driven an unprecedented revolution in biological sciences for its role in elucidating gene functions. A multitude of software has been developed for the design and analysis of CRISPR/Cas experiments, including predictive tools to design optimally guide RNA for various experimental operations. Different in silico sgRNA design tools have various application scenarios and identifying the optimal design tools can often be a challenge. This paper describes the sgRNA design workflow in experiments, the classification of sgRNA designers, previously published benchmarking work of in silico designers, and the criteria involved how to select an sgRNA web server. Through basic testing, this paper comprehensively overviews and compares the features of 43 web server designers to provide a reference for the readers. Ultimately, the project developed an integrated platform, called Aid-TG, which helps users find appropriate tools quickly.

Keywords CRISPR/Cas Aid-TG gene editing sgRNA design web server

Corresponding Author(s): Lei MA

Just Accepted Date: 20 December 2022 Online First Date: 09 February 2023

Cite this article:

Qianqian YANG,Lei MA. A PLATFORM TO AID SELECT THE OPTIMAL TOOL TO DESIGN GUIDE RNAS[J]. Front. Agr. Sci. Eng. , 09 February 2023. [Epub ahead of print] doi: 10.15302/J-FASE-2022479.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2022479
https://academic.hep.com.cn/fase/EN/Y/V/I/0

Fig.1 (a) Schematic diagram showing the workflow of sgRNA design for CRISPR/Cas adaptive immune system. (b) The classification of in silico sgRNA design tools. They are sequence pairing-based (1), feature scoring-based (2), and machine learning-based (3), respectively.

Tab.1 Comparison of the features of sequence pairing-based sgRNA design websites

Tab.2 Comparison of the features of Feature scoring-based design websites

Tab.3 Comparison of the features of machine learning-based design websites

Fig.2 The display of Aid-TG’s mainly panel. Here, select your matching options and click “START”, then the recommend designer will be returned. And you can click the “Click here” to go directly to the usage page of the recommend tool^[²¹^].

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