Author: Vipin Menon, BIG Lab Original: May 2016 | Modernized: 2026 Language: Python 3.8+
CINDEL calculates predicted activity scores for CRISPR-Cpf1 (Cas12a) guide RNAs. It helps researchers identify the most active guides from a pool of candidates.
The scoring model combines:
- RNA free energy of the 23-bp target region (via ViennaRNA)
- Global nucleotide composition (A, AC, CG, CC, TA counts)
- Position-dependent nucleotide features (50 coefficients for specific positions)
The final score is a logistic-transformed linear combination of these features, returning a value between 0 (inactive) and 1 (highly active).
| Property | Requirement |
|---|---|
| Total length | 27 bp |
| PAM (pos 0–3) | TTTV where V = A, G, or C |
| Target (pos 4–27) | 23 bp |
Valid PAM sequences: TTTA, TTTG, TTTC
git clone https://github.com/vipinmenon1989/CINDEL.git
cd CINDELpython3 -m venv venv
source venv/bin/activate # macOS / Linux
venv\Scripts\activate # Windowspip install -r requirements.txtNote: ViennaRNA must be installed separately via conda (recommended):
conda install -c bioconda viennarna
Score all guide RNAs in a CSV file. The input must have a header row with columns sequence_id and sequence.
python CINDEL.py -a input.csv
python CINDEL.py -a input.csv --output results.csvInput CSV format:
sequence_id,sequence
guide_001,TTTACGTAGCTAGCTAGCTAGCTAGCT
guide_002,TTTGCGATCGATCGATCGATCGATCGA
Output CSV format:
sequence_id,sequence,score
guide_001,TTTACGTAGCTAGCTAGCTAGCTAGCT,0.734521
guide_002,TTTGCGATCGATCGATCGATCGATCGA,0.412038
Score one 27-bp guide RNA directly on the command line.
python CINDEL.py -b TTTACGTAGCTAGCTAGCTAGCTAGCTOutput:
Sequence : TTTACGTAGCTAGCTAGCTAGCTAGCT
PAM : TTTA
Target (23 bp) : CGTAGCTAGCTAGCTAGCTAGCT
CINDEL Score : 0.734521
Scan a long genomic sequence for all valid Cpf1 guide RNA candidates (must be > 100 bp).
python CINDEL.py -c ATCGATCGATCGATCG...LONG_SEQUENCE...Output: A ranked table of all candidate guides sorted by score (highest first).
| Option | Description |
|---|---|
-a, --batch |
Batch mode: path to input CSV file |
-b, --single |
Single mode: one 27-bp sequence string |
-c, --find |
Finder mode: long genomic sequence to scan |
-o, --output |
Output CSV path for batch mode (default: Score.csv) |
-v, --verbose |
Enable verbose/debug logging |
-h, --help |
Show help message and exit |
| Package | Purpose | Install |
|---|---|---|
| ViennaRNA | RNA secondary structure free energy | conda install -c bioconda viennarna |
| Python ≥ 3.8 | Runtime | python.org |
See requirements.txt for the full list.
CINDEL/
├── CINDEL.py # Main scoring tool
├── requirements.txt # Python dependencies
├── README.md # This file
└── .gitignore # Git ignore rules
If you use CINDEL in your research, please cite the original work from the BIG Lab.
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