CRISPR-PLANT v2

How to Use the Search Function

You can easily access the CRISPR-PLANT v2 dataset in three simple steps:

1. Select plant species and gene locus ID of interest:

   Check the genome annotation sources used to ensure ID/version compatibility.

   
2. View results. Each row includes:
   • seqID: Format: Chr:start-end:strand
   • class: Specificity group (e.g., A0, B2)
   • minMM_GG / minMM_AG: Mismatch count to off-targets
   • seq: gRNA spacer sequence (20 nt)
   • PAM: Including 7 bp flanking sequence
   • strand: Target strand (+ or -)
   • location: Genomic feature targeted (exon, intron, etc.)
   
3. Press the "Download CSV" button to export your data search.

Spacer Classification

Spacers are classified to reduce off-target risk:

• Class A: 1 mismatch in the 10 bp seed + 3 more elsewhere
• Class B: 1 mismatch in the 15 bp seed + 3 more elsewhere
• Subgroups (0, 0.1, 1, 2) indicate NAG off-target risk

Recommended: A0, A0.1, B0, B0.1 as highly specific spacers.

Learn more in the About Us section.

Bioinformatic Pipeline

All NGG and NAG PAM-adjacent spacers are extracted genome-wide and compared. Spacers are grouped by mismatch count and seed region differences. A1–B2 spacers are backups when A0–B0.1 are unavailable.

Genome Annotation Sources

Working with a different genome or Cas variant? Clone our pipeline from the GitHub repository and adapt it to your needs.