ClinASO

ClinASO — A comprehensive web platform for Gapmer Antisense Oligonucleotide (ASO) design and analysis. Developed by the Bioinformatics team at Yunnan University.

Live Demo: www.gapmerasodesign.com

• 🧬 Gapmer ASO Design — Design gapmer ASOs with customizable parameters (length, GC content, count, selection priority) across multiple species
• 🔗 Homology Analysis — Evaluate ASO compatibility across 6 species (Human, Mouse, Rat, Pig, Crab-eating Macaque, Rabbit, Guinea Pig) using RNAhybrid
• 🧪 SNP Analysis — Investigate SNP variants within ASO target regions using dbSNP v157
• 🎯 Off-Target Analysis — Predict potential off-target binding sites across the human genome (GRCh38)

ClinASO/
├── web/
│   ├── app/              # Flask backend (app.py) + frontend files
│   │   ├── app.py        # Main Flask application
│   │   ├── index.html    # Frontend HTML
│   │   ├── script.js     # Frontend JavaScript
│   │   └── style.css     # Frontend styles
│   └── static/           # Images and static assets
├── asodesigner/          # Core ASO design pipeline
│   ├── aso_design2.sh    # Main design pipeline script
│   ├── scr/              # Python scripts for each design step
│   ├── scr_b/            # Backup scripts
│   └── text/             # Species mapping & PWM data
├── homology/             # Cross-species homology analysis
│   ├── _homologyanalysis.sh
│   ├── appdesignASO.py   # Extract ortholog gene sequences
│   └── homology_report.py # PDF report generator
├── snp/                  # SNP analysis module
│   ├── _snp.sh
│   └── plot.py           # PDF report with SNP visualization
├── offtarget/            # Off-target analysis module
│   ├── _offtarget.sh
│   └── _plot.py          # PDF report generator
├── config/
│   └── genetic-analysis.service.example  # Systemd service config
└── docs/                 # Additional documentation

git clone https://github.com/wusuw/ClinASO.git
cd ClinASO

# Create the main environment
conda create -n clinaso python=3.10 -y
conda activate clinaso

# Install Python dependencies
pip install flask flask-cors reportlab pillow biopython

conda create -n RNAhybrid -c bioconda rnahybrid -y

# Ubuntu/Debian
sudo apt update
sudo apt install -y nginx bedtools bcftools

# CentOS/RHEL
sudo yum install -y nginx bedtools bcftools

Genomic reference files are too large to include in this repository. You need to download them separately:

• Download from NCBI
• Required files: genomic.fna, genomic.gtf
• Place in: asodesigner/reference/human/

• Download from NCBI
• Required files: GRCm39_genomic.fna, GRCm39_genomic.gtf
• Place in: asodesigner/reference/mouse/

• Download from NCBI
• Required files: GRCr8_genomic.fna, GRCr8_genomic.gtf
• Place in: asodesigner/reference/rat/

• Download from NCBI
• Required files: GCF_000003025.6_Sscrofa11.1_genomic.fna, GCF_000003025.6_Sscrofa11.1_genomic.gtf
• Place in: asodesigner/reference/pig/

• Download from NCBI
• Required files: genomic.fna, genomic.gtf
• Place in: asodesigner/reference/crab_eating_macaque/

• Download from NCBI
• Required files: GCF_964237555.1_mOryCun1.1_genomic.fna, GCF_964237555.1_mOryCun1.1_genomic.gtf
• Place in: asodesigner/reference/rabbit/

• Download from NCBI
• Required files: GCF_034190915.1_mCavPor4.1_genomic.fna, GCF_034190915.1_mCavPor4.1_genomic.gtf
• Place in: asodesigner/reference/guinea_pig/

• Download from NCBI HomoloGene
• Place in: asodesigner/text/gene_orthologs

# Human SNP VCF
wget https://ftp.ncbi.nlm.nih.gov/pub/snp/latest_release/VCF/GCF_000001405.40/GCF_000001405.40.gz
wget https://ftp.ncbi.nlm.nih.gov/pub/snp/latest_release/VCF/GCF_000001405.40/GCF_000001405.40.gz.tbi
# Place in: snp/

# Create gene2 fasta for off-target analysis (requires bedtools)
# You need to build this from the human genome GTF + FASTA
# Place in: offtarget/GRCh38.gene2.fasta

The final directory structure should look like:

asodesigner/reference/
├── human/
│   ├── genomic.fna
│   └── genomic.gtf
├── mouse/
│   ├── GRCm39_genomic.fna
│   └── GRCm39_genomic.gtf
├── rat/
├── pig/
├── crab_eating_macaque/
├── rabbit/
└── guinea_pig/

Edit web/app/app.py and update:

# Email configuration (for sending results)
SMTP_SERVER = 'smtp.example.com'
SMTP_PORT = 465
SMTP_USERNAME = 'your_email@example.com'
SMTP_PASSWORD = 'your_smtp_password'
FROM_EMAIL = 'your_email@example.com'

sudo mkdir -p /asodesigner/outfile /homologyanalysis/outfile /snp/outfile /offtarget/outfile
sudo chmod -R 777 /asodesigner/outfile /homologyanalysis/outfile /snp/outfile /offtarget/outfile

All shell scripts use absolute paths. If your installation directory differs from /, update the paths in:

• asodesigner/aso_design2.sh
• homology/_homologyanalysis.sh
• snp/_snp.sh
• offtarget/_offtarget.sh

server {
    listen 80;
    server_name your-domain.com;

    # Frontend static files
    location / {
        root /path/to/ClinASO/web;
        index index.html;
        try_files $uri $uri/ /index.html;
    }

    # Flask API proxy
    location /submit_design /analyze_sequence /analyze_snp /analyze_offtarget /queue-status {
        proxy_pass http://127.0.0.1:5000;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_read_timeout 300s;
    }

    # Static assets
    location /static/ {
        alias /path/to/ClinASO/web/static/;
        expires 30d;
    }
}

# Copy and edit the systemd service file
sudo cp config/genetic-analysis.service.example /etc/systemd/system/genetic-analysis.service

# Edit the ExecStart path in the service file to match your installation
sudo nano /etc/systemd/system/genetic-analysis.service

# Enable and start
sudo systemctl daemon-reload
sudo systemctl enable genetic-analysis
sudo systemctl start genetic-analysis

# Check status
sudo systemctl status genetic-analysis

Access the web interface at http://your-domain.com:

1. Gapmer Design — Enter a gene symbol, select parameters, and submit. Results (ASO candidates) will be emailed as Excel attachments.
2. Homology Analysis — Provide an ASO sequence and select target species. A PDF report with RNAhybrid alignment results will be emailed.
3. SNP Analysis — Provide a gene name and ASO sequence. A PDF report with SNP variant information will be emailed.
4. Off-Target Analysis — Provide a target gene and ASO sequence. A PDF report with potential off-target binding sites will be emailed.

If you use ClinASO in your research, please cite:

ClinASO: a computational-experimental platform for rapid drug discovery of gapmer antisense oligonucleotides

This project is licensed under the MIT License - see the LICENSE file for details.

• Developer: ShunKai Chen
• Principal Investigators: Yunkun Dang, Fan Lai
• Email: chenshunkai@stu.ynu.edu.cn
• Institution: School of Life Sciences, Yunnan University, Kunming, China