Introduction
Welcome to the documentation for the SPACER Web interface — your guide to designing high-performance CRISPR guide RNAs for nucleic acid diagnostics.
What is SPACER?
SPACER (Spacer Profiling and Activity-driven crRNA Efficacy Ranking) is a high-performance Rust library and web application for designing CRISPR guide RNAs (crRNAs). It targets both Cas12 and Cas13 enzyme families, which are the workhorses of CRISPR-based nucleic acid detection systems like SHERLOCK and DETECTR.
Unlike general-purpose CRISPR design tools that focus on gene editing, SPACER is purpose-built for diagnostic applications — where the goal is to maximize detection sensitivity and specificity, not to edit genomes.
Key Features
| Feature | Description |
|---|---|
| Multi-enzyme support | Cas12 (DNA-targeting) and Cas13 (RNA-targeting) families |
| Composite scoring | Weighted 0–100 score combining GC content, homopolymers, activity, and structure |
| Tier classification | Automatic ranking into Excellent, Good, Fair, and Poor tiers |
| Quality flags | Detailed warnings for each guide explaining score deductions |
| AI activity prediction | Optional ML models — EasyDesign (Cas12) and ADAPT (Cas13) — for predicting guide activity |
| RNA structure analysis | Optional Vienna RNA folding for secondary structure scoring |
| Primer design | RPA primer generation for amplification workflows |
| Multiple export formats | CSV, TSV, JSON, and FASTA output |
How It Works
When you submit a sequence through this web app, it is sent to the SPACER API which delegates to the core analysis engine. The engine handles all scoring, ML prediction, structure analysis, and primer design.
Getting Help
If you have questions, feedback, or run into issues, reach out through our contact page.