CRISPy-web 3.0: A unified platform for multi-modal guide RNA design for CRISPR and TnpB genome editing applications
Year: 2025
Type: article
Abstract: CRISPy-web is an interactive web-based platform designed for rational guide RNA design in CRISPR-Cas9-based genome editing systems. Here, we present CRISPy-web 3.0 (https://crispy.secondarymetabolites.org/), an upgraded and versatile version that extends its functionality beyond classical Cas9-based systems. This version integrates support for diverse genome editing systems, including Cas9, CRISPR interference (CRISPRi), and TnpB/ωRNA. The redesigned interface enables users to toggle between multiple editing modes, select target regions such as ORFs or 5' UTRs, and visualize strand orientation, off-targets, and predicted mutation outcomes. It also incorporates scoring systems that evaluate guide RNA efficiency and specificity based on mismatch tolerance, positional context, and PAM requirements for CRISPR-Cas9-based applications. With an improved user interface design, enhanced backend scalability, and modular support for customizable inputs, CRISPy-web 3.0 provides a comprehensive and extensible platform for guide RNA design, enabling genome editing across a broader range of prokaryotic systems, including both CRISPR and TnpB.
Authors: Sihan Yang, Zupeng Cai, Natalie Chia, Jing Luo, Tilmann Weber, Kai Blin, Yaojun Tong
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,500
Funders: National Natural Science Foundation of China, Science and Technology Commission of Shanghai Municipality, Shanghai Jiao Tong University, Novo Nordisk Fonden, Key Technologies Research and Development Program, National Key Research and Development Program of China, Scientific and Innovative Action Plan of Shanghai
OpenAlex ID: W4415220163