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Getting Started

Launching the Application

Step 1: Open the Application

macOS: Open Applications folder → Double-click the app

The main window will appear with two tabs: Matching and Dynamite

Main Interface Overview

DynamiR Main Interface

Understanding Input Modes

Each input field (microRNA, mRNA, Seed) supports three entry methods. You'll see radio buttons to choose:

🔘 Mode 1: Database ID

Database ID Input Mode

What it does: Fetches sequence directly from online database
Best for: Quick access to known sequences
Examples: - microRNA IDs: MIMAT0000062 (mmu-let-7a) - mRNA IDs: NM_000546.6 (TP53 gene)

📁 Mode 2: File Upload

File Upload Mode

What it does: Reads sequence from your computer
Best for: Local data, custom sequences
Supported formats: - FASTA: .fa, .fasta (plain sequence) - GenBank: .gb, .gbk (annotated sequence)

✏️ Mode 3: Direct Sequence

Direct Sequence Input Mode

What it does: Analyzes text you type directly
Best for: Quick tests, short sequences
Notes: Whitespace is ignored, auto-converted to uppercase

Choosing Your Analysis Mode

📍 Use MATCHING Mode When:

  • You have a specific microRNA in mind
  • You want to know if it binds to your target mRNA
  • You need detailed alignment visualization
  • You're validating a known interaction

✅ Speed: Instant (< 1 second)
✅ Output: Detailed alignments + statistics

🔍 Use DYNAMITE Mode When:

  • You want to discover which microRNAs bind your mRNA
  • You have a target gene but unknown regulators
  • You need to see all possible microRNA candidates
  • You're doing exploratory research

⏱️ Speed: ~1-5 minutes (scans the 48,860 microRNAs of the miRBase DataBase)
✅ Output: Ranked list of potential binders

Your First Analysis: Matching Mode

Step 1: Select microRNA

Select microRNA for Matching Mode

Enter microRNA ID: MIMAT0007560 (mmu-mir-30a)

Step 2: Select mRNA

Select mRNA for Matching Mode

Enter mRNA GenBank ID: NM_008539 (mouse SMAD1)

Step 3: Set Seed Region

Set Seed Region

This is the standard seed region - usually 2-7 or 2-8

Step 4: Run Analysis

Click [Parse] button and wait for results

Step 5: View Results

Results appear in the right panel showing: - Number of binding sites found - Position of each site in mRNA - Base pairing visualization - Statistics (Watson-Crick pairs, wobble pairs)

Matching Mode Results Display

Step 6: Download (Optional)

Click 💾 button to save results to a text file

Download Results Button

Your First Analysis: Dynamite Mode

Step 1: Select mRNA

Select mRNA for Dynamite Mode

Enter mRNA GenBank ID: NM_008539 (mouse SMAD1)

Step 2: Set Seed Region

Set Seed Region

Step 3: Run Scan

Click [Parse] button

Step 4: Wait for Results

A progress popup shows:

Scanning Progress Popup

Step 5: View Results Table

After scanning completes, you see a table:

Dynamite Mode Results Table

Step 6: Download

Click 💾 to export the complete table

Download Dynamite Results

Key Concepts to Remember

🧬 What is a "Seed Region"?

The seed region (typically positions 2-7 of the microRNA) is the most critical for binding. In this tool: - Positions are 1-indexed (position 1 is the first nucleotide) - Typical range: 2-7 (most important for binding) - Alternative: 2-8 (more stringent) - This region MUST match perfectly for a binding site to be detected

📊 What Do the Results Mean?

  • Position: Where in the mRNA the binding site starts (1-indexed)
  • Watson-Crick Pairs: Normal, strong base pairings (A-U, C-G)
  • Wobble Pairs: Special G-U pairings (weaker but still valid)
  • Bind%: Percentage of microRNA that pairs with mRNA
  • Score: Total pairing strength (higher = better binding)

🔄 DNA vs RNA

  • The tool automatically converts DNA (with T) to RNA (with U)
  • You can paste either format - it will be handled correctly

Next Steps