🧬 CRISPR Efficiency Predictor

Predict guide RNA cutting efficiency for SpCas9 based on sequence features. Uses a simplified model inspired by Doench et al. 2014 & 2016.

Guide RNA (20‑nt spacer) or full sequence with NGG PAM

Organism (for GC content preference)

💡 Instructions: Enter a 20‑nt guide sequence (or paste the full target with NGG PAM). The tool will extract the guide, compute features, and estimate efficiency.

📖 How the score is calculated

Based on published models, we consider several features:

GC content: Optimal range 40-70%. Too low or too high reduces efficiency.
Position 1 (5' base): G is preferred (higher efficiency).
Position 20 (base adjacent to PAM): G is preferred.
Homopolymer runs: Runs of 4+ same nucleotides reduce efficiency.
Poly‑T stretches: T-rich regions are disfavoured.

The overall score is a weighted sum of these features, normalised to 0‑100. Scores > 70 are considered high efficiency; 40-70 moderate; <40 low.