DynamiR

Welcome to DynamiR

🧬 What This Tool Does

DynamiR is a desktop application designed for researchers and biologists to identify and analyze potential binding sites where microRNAs can attach to messenger RNA (mRNA) sequences.

Key Capabilities:

Direct Analysis (Matching Mode): Analyze a specific microRNA against a target mRNA to find exact binding positions
Database Scanning (Dynamite Mode): Scan all ~48,860 known microRNAs against your target mRNA in one analysis
Multiple Input Methods: Load sequences from files (FASTA, GenBank) or directly from online databases (miRBase, NCBI)
Results: Get detailed binding site information including positions, pairing statistics, and alignment visualizations
Export Functionality: Save your analysis results for further processing or sharing

⚡ Quick Start

Download & Installation

📥 Download for macOS - Version 1.0 - Available

First Steps

Install the application for your operating system
Launch the application
Choose a Mode - This step can be done in two ways:
Use Matching Mode to test a specific microRNA
Use Dynamite Mode to discover all possible microRNA binders
Enter Your Data: Provide sequences via files or database IDs
Run Analysis and view results
Export your findings

� Video Demonstration

Watch this video to see DynamiR in action:

Full Demo on YouTube - See how to use all analysis modes and interpret results.

�🎯 Use Cases

Research & Discovery

Identify potential microRNA regulators for your target genes
Validate predicted binding sites computationally
Discover off-target microRNA interactions

Validation

Confirm microRNA-mRNA interactions predicted by other tools
Test multiple seed regions to understand binding specificity
Compare results across different analysis parameters

Educational

Learn how microRNA binding prediction works
Understand seed-region importance in sequence matching
Visualize RNA duplex alignments

📚 Documentation

Installation Guide - Setup instructions for all platforms
Getting Started - First time users guide
Matching Mode - Direct microRNA-mRNA analysis
Dynamite Mode - Database-wide scanning
Biological Concepts - Understanding the biology
How It Works - System architecture and workflows

💡 Key Features

✅ Dual Analysis Modes - Choose between focused analysis or broad screening
✅ Multiple Input Options - Files, database IDs, or direct sequence entry
✅ Visual Alignments - See base pairing details at each binding site
✅ Quick Export - Save results in text format
✅ Responsive Interface - User-friendly experience
✅ Quality - Tool with error handling

🔬 What Makes This Different

This tool implements seed-based matching with Watson-Crick pairing detection and wobble pair recognition. It uses proper bioinformatic algorithms to identify realistic binding scenarios.

Seed Region Matching: The default seed region is positions 2-7 of the microRNA - this is the critical region for binding stability. You can customize the seed region to match your research needs.

Extended Analysis: Full duplex alignment scoring shows additional pairing strength beyond the seed region.

📖 Learn More

New to microRNA biology? Start with Biological Concepts
Want to understand the matching algorithm? Read How It Works
Ready to analyze? Follow Getting Started

🤝 Support

For questions, issues, or suggestions: - 📧 Email: remi.hocquetmartin@icloud.com - 🐛 Report bugs: GitHub Issues