A lightweight Python tool for identifying and ranking candidate CRISPR-Cas9 guide RNAs from user-provided DNA sequences. The program scans both DNA strands for SpCas9-compatible target sites containing the NGG PAM motif and evaluates guide quality using several commonly considered design features.
- Identification of candidate SpCas9 guide RNAs (20 nt + NGG PAM)
- Analysis of both forward and reverse DNA strands
- GC content calculation and optimisation scoring
- Detection of homopolymer runs that may reduce guide performance
- Simple self-complementarity assessment to flag potential secondary structure formation
- Restriction enzyme site detection (EcoRI, BamHI and HindIII)
- Automatic ranking of guides using a composite quality score
- Export of results as a CSV file for downstream analysis
- Support for direct sequence input or FASTA file input
- Preliminary CRISPR guide design for gene editing projects
- Educational demonstrations of guide RNA selection principles
- Rapid screening of candidate target regions before using dedicated CRISPR design platforms
- Bioinformatics training and workflow development
For each detected guide RNA, the program reports:
- Genomic position
- Strand orientation
- Guide sequence
- PAM sequence
- GC percentage
- Homopolymer status
- Self-complementarity score
- Restriction enzyme site warnings
- Overall guide quality score
Results are automatically ranked from highest to lowest predicted quality and exported in CSV format.
This tool provides a simplified guide quality assessment and is intended for educational and exploratory use. Comprehensive CRISPR guide design should include genome-wide off-target analysis, species-specific genome annotation and experimental validation.