CRISPy-web 3.0: Now Supporting Multi-Modal Genome Editing
What's New
CRISPy-web 3.0 is a major upgrade that transforms the platform from a Cas9-only tool into a unified, multi-modal guide RNA design suite. The new version supports three distinct genome editing systems:
- Cas9 – The classic CRISPR-Cas9 system
- CRISPRi – CRISPR interference for transcriptional repression
- TnpB/ωRNA – A compact, emerging genome editing system using ωRNA guides
Key Features
- Multi-mode toggle – Switch seamlessly between Cas9, CRISPRi, and TnpB design modes
- Strand-aware design – Visualize and select template vs. non-template strand targeting (critical for bacterial CRISPRi efficiency)
- Flexible target selection – Choose ORFs, 5′ UTRs, or promoter regions
- Advanced scoring – Evaluate guide RNA efficiency and specificity using mismatch-tolerant algorithms tailored for prokaryotic systems
- Off-target visualization – See predicted off-targets and mutation outcomes directly in the interface
- Custom genome support – Upload and work with user-provided microbial genomes in GenBank format
Why It Matters
Most existing tools are locked into Cas9-only workflows. CRISPy-web 3.0 bridges the gap for researchers working with non-model organisms and emerging editing technologies. In particular, we added support for the compact TnpB system, which offers programmable DNA targeting with minimal protein size, ideal for challenging in vivo applications.
Try It Now
Access the platform at: https://crispy.secondarymetabolites.org/
Reference: Yang et al., "CRISPy-web 3.0: A unified platform for multi-modal guide RNA design for CRISPR and TnpB genome editing applications," Synthetic and Systems Biotechnology, Volume 11, March 2026. DOI: 10.1016/j.synbio.2025.10.003