DNAnalyzer

<div align="center"> <h3>Next-Generation On-Device DNA Insights</h3> <p><i>Private. Precise. Powered by AI.</i></p>

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About DNAnalyzer

DNAnalyzer is a biotechnology research and deployment company revolutionizing genomic analysis through AI-powered, privacy-first technology. Supported by Anthropic for Startups, our mission is to democratize DNA analysis by delivering enterprise-grade genomic insights through secure on-device computation.

Founded by Piyush Acharya, DNAnalyzer brings together 46 leading computational biologists and computer scientists from Microsoft Research, the University of Macedonia, and Northeastern University.

Our groundbreaking work has been presented at Y Combinator's Mini YC and reached semifinals (top 10%) for a16z's $1M investment.

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Why DNAnalyzer Matters

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| Industry Standard | DNAnalyzer's Innovation | |---|---| | $100 average cost for DNA sequencing | Completely Free analysis | | Up to $600 for basic health insights | Universally accessible, empowering underserved communities worldwide* | | 78% of companies share genetic data with third parties | 100% Private: All computation happens locally on your device | | Data breaches compromise millions (23andMe: 6.9M users in 2023) | Zero central storage: Your genetic data never leaves your device |

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"Unlike a password, compromised genetic data is permanently exposed. You cannot change it."

<small>*Excluding testing costs. We're developing an affordable in-house testing kit to eliminate this final barrier.</small>

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Core Capabilities

<table> <tr> <td width="33%" align="center"> <strong>Codon & Protein Detection</strong><br> Rapidly identifies protein-coding regions, amino acid chains, and critical genomic indicators with unprecedented accuracy. </td> <td width="33%" align="center"> <strong>GC-rich Region Analysis</strong><br> Precisely pinpoints genomic promoter areas with significant biological implications (45-60% GC-content). </td> <td width="33%" align="center"> <strong>Neurological Genomics</strong><br> Detects genetic markers associated with neurological conditions including autism, ADHD, and schizophrenia. </td> </tr> <tr> <td width="33%" align="center"> <strong>Promoter Element Identification</strong><br> Locates key transcription initiation sequences (BRE, TATA, INR, DPE) with surgical precision. </td> <td width="33%" align="center"> <strong>Multi-format FASTA Integration</strong><br> Seamlessly supports comprehensive DNA database analysis from uploads or external sources. </td> <td width="33%" align="center"> <strong>Met CLI Automation</strong><br> Harnesses a powerful CLI interface for scripting, automation, and enterprise-scale analysis tasks. </td> </tr> <tr> <td width="33%" align="center"> <strong>Privacy-First Ancestry Insights</strong><br> Estimates continental origin using on-device reference panels without compromising privacy. </td> <td></td> <td></td> </tr> </table> <br>

See the Ancestry Snapshot guide for detailed usage instructions.

New: Interactive web dashboard for real-time visualization is now available under web/dashboard, seamlessly communicating with the local REST API at /api.

Intelligent Natural Language Reports

When an OpenAI key is available, each CLI run now produces two narratives immediately after the metrics:

• Researcher Report – Technical interpretation with references to the detected GC windows, ORFs, PRS coverage, etc.
• Layperson Report – Plain-language explainer that highlights the most actionable findings.

Set OPENAI_API_KEY (or AI_PROVIDER=openai plus the corresponding key) before launching DNAnalyzer and the summaries will appear in the terminal and be saved to analysis_output/.../reports/. Use --no-ai if you want to skip the call for a particular run.

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Quickstart Guide

Ready to unlock your genomic insights? Begin precision DNA analysis in seconds:

# Clone the repository
git clone https://github.com/VerisimilitudeX/DNAnalyzer.git

# Navigate to project directory
cd DNAnalyzer

# Install dependencies
./gradlew build

Enable AI summaries (optional): export your API key before running the CLI, e.g.

export OPENAI_API_KEY=sk-...
# optionally pick a model
export OPENAI_MODEL=gpt-4o-mini

Pass --no-ai if you prefer a run without contacting the API; all analytic outputs still generate.

🚀 NEW: Intuitive Launch Script

We've transformed DNAnalyzer's user experience! Say goodbye to complex command-line options:

# Simple preset modes
./easy_dna.sh your_file.fa basic      # Standard analysis
./easy_dna.sh your_file.fa detailed   # Comprehensive analysis  
./easy_dna.sh your_file.fa mutations  # Generate mutations
./easy_dna.sh your_file.fa all        # Complete suite
./easy_dna.sh your_file.fa custom     # Interactive mode

# Or use the traditional Java method
java -jar build/libs/DNAnalyzer-1.2.1.jar your_file.fa

easy_dna.sh automatically uses a feature-complete jar from build/libs/ when available, falls back to ./gradlew run, and warns if only the legacy basic jar is present. Override the jar path with DNANALYZER_JAR=/path/to/dnanalyzer.jar if needed.

📁 NEW: Intelligent Output Organization

All generated files are automatically organized in a clean, intuitive directory structure:

output/dnanalyzer_output_{filename}_{timestamp}/
├── charts/          # Quality control and analysis visualizations (PNG)
├── sequences/       # Generated mutations and processed sequences (FASTA)
└── reports/         # Comprehensive analysis reports and summaries (HTML)

🎯 NEW: Smart Analysis Profiles

Leverage predefined profiles tailored to your workflow:

# Select analysis profiles optimized for common use cases
java -jar build/libs/DNAnalyzer-1.2.1.jar --profile research your_file.fa
java -jar build/libs/DNAnalyzer-1.2.1.jar --profile clinical your_file.fa
java -jar build/libs/DNAnalyzer-1.2.1.jar --profile mutation your_file.fa

# Available profiles: basic, detailed, quick, research, mutation, clinical
# List available presets directly from the CLI
java -jar build/libs/DNAnalyzer-1.2.1.jar --profile list

📚 Documentation

• Getting Started Guide - Essential setup and configuration
• Enhanced Features Guide - NEW! Comprehensive guide to all user experience improvements
• Command Reference - Complete command-line options and examples
• Changelog - NEW! Detailed release notes and version history

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Polygenic Health-Risk Scores

DNAnalyzer now features an advanced polygenic risk score calculator alongside engaging trait predictions. Simply provide your 23andMe data file with a CSV of SNP weights to compute personalized scores:

./gradlew run --args='--23andme my_data.txt --prs assets/risk/heart_disease_prs.csv sample.fa'
java -jar build/libs/DNAnalyzer-1.2.1.jar --23andme my_data.txt --prs assets/risk/heart_disease_prs.csv sample.fa

The CLI now parses the standard tab-delimited 23andMe export, aligns it with each provided weight table, and reports the raw and normalized contribution of every SNP in the trait. Missing or uncallable variants are clearly identified so you can assess coverage before acting on a score. See the Polygenic Risk Scoring guide for a detailed walkthrough and example outputs.

Trait predictions and risk scores are displayed following standard DNA analysis. Disclaimer: Trait predictions are provided for educational purposes only and should not be used for medical or health decisions.

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REST API

The project now ships with a production-ready Spring Boot service that powers the web dashboard and external integrations. Start it locally with:

./gradlew bootRun

The API is exposed under /api/v1 and returns JSON. Key endpoints include:

| Endpoint | Method | Description | | --- | --- | --- | | /api/v1/status | GET | Health check and version metadata | | /api/v1/analyze | POST (multipart) | Run the full analysis pipeline on an uploaded FASTA/FASTQ/plain-text sequence | | /api/v1/base-pairs | POST (JSON) | Return base pair counts, percentages, and GC content for a sequence | | /api/v1/reading-frames | POST (JSON) | Identify open reading frames in forward and reverse directions | | /api/v1/find-proteins | POST (JSON) | Predict candidate proteins (top 10 by length) |