Al-Awal Documentation

Quick Start

1. Request Access

Contact us to request access to the Al-Awal platform. Once approved, you will receive your credentials to log in.

2. Load Your Sequence

Three ways to input your DNA sequence:

• Manual entry: Paste directly into the sequence editor
• FASTA upload: Click "Upload" to load .fasta, .fa, or .fna files
• Sample sequences: Use built-in examples (Insulin B, GFP) to explore

3. Run Analysis

Click "Analyze & Visualize" to generate the codon map with pause scores.

4. Optimize

Use "Auto-Optimize All" for full sequence optimization, or click individual codons for targeted adjustments.

5. Export Results

Download your optimized sequence in FASTA, TXT, JSON, or CSV format.

Core Concepts

Pause Score

The pause score (measured in milliseconds) represents the predicted time a ribosome pauses at each codon during translation. Lower scores indicate faster translation.

DAIS (Dynamic Assurance Indexing of Sequence)

Our proprietary quality index that evaluates overall sequence optimization:

Optimization Models

Supported Organisms

Sequence Editor

Input Validation

The platform automatically validates your sequence:

• ✓ Start codon: Must begin with ATG
• ✓ Stop codon: Must end with TAA, TAG, or TGA
• ✓ Reading frame: Length must be divisible by 3
• GC Content: Displayed as percentage

Accepted Characters

Only A, G, T, C nucleotides are accepted. Other characters are automatically filtered.

Canvas Navigation

• Pan: Click and drag on empty canvas
• Zoom: Mouse scroll or pinch gesture
• Select codon: Click on any codon node
• Multi-select: Shift + click

Codon Visualization

Each codon is displayed as an interactive node showing:

• Position number (#1, #2, #3...)
• Amino acid (single letter code)
• Codon triplet (e.g., ATG, GCA)
• Pause score (in milliseconds)

Color Coding

Codons are colored based on their pause score:

• ● Green: Fast translation (low pause)
• ● Yellow: Moderate pause
• ● Red: Slow translation (high pause - optimization target)

Optimization

Auto-Optimize All

Optimizes the entire sequence in one click using the selected model and organism settings.

Requirements:

• Must be logged in
• Sequence must pass validation

Single Codon Optimization

Click any codon to see:

• Current pause score
• Alternative codon suggestions
• Improvement percentage for each option
• AI recommendation

Note: Only synonymous codons are suggested (same amino acid, different nucleotides).

3D Visualization

Protein Structure Prediction

Generate predicted 3D protein structure using ESMFold technology.

To use:

1. Load your sequence
2. Go to Tools → 3D Structure
3. Wait for folding prediction (~10-30 seconds)

Heatmap Overlay

Pause scores are mapped onto the 3D structure:

• ● Green regions: Fast translation
• ● Red regions: Ribosomal pause zones

Critical Residue Labels

Residues in the top 5% of pause scores are labeled with:

• Amino acid and position
• Codon triplet
• Pause time in milliseconds

Kinetics Chart

The kinetics chart displays pause scores for all codons as an interactive bar graph.

Features

• Horizontal scroll: Navigate long sequences
• Hover tooltips: See detailed codon information
• Critical peaks: Marked in red with warning indicators
• Click to select: Clicking a bar selects that codon on the canvas

AI Peak Analysis

Click "Analyze Peaks" for AI-powered insights on:

• Why certain positions have high pause scores
• Recommendations for optimization
• Potential impact on protein folding

Mutation Comparison

Compare kinetic profiles between two sequences:

1. Go to Mutation Analysis tab
2. Paste your Wild-Type sequence
3. Paste your Mutant sequence
4. Click "Compare Impact"

The tool identifies:

• Position of mutations
• Change in pause scores
• Predicted effect on translation efficiency

Reports & Export

Optimization Report

After optimization, generate a detailed report showing:

• Before/after comparison charts
• Performance gain percentage
• Critical pauses fixed count
• Estimated expression improvement
• Total time saved (milliseconds)

Export Formats

Project Management

Save Projects

• Click Save to store your project in the cloud
• Projects include: sequence, all codons, notes, and layout

Load Projects

• Click Load to see your saved projects
• Projects show name and last modified date

Save As

Create a copy of your current project with a new name

Undo/Redo

• Supports up to 20 levels of undo
• Keyboard shortcuts: Ctrl+Z (undo), Ctrl+Shift+Z (redo)

Notes

Add annotations to your sequence:

1. Click "Add Note" in the Tools section
2. Position the note on the canvas
3. Connect it to any codon using the bottom handle
4. Double-click to edit text

Keyboard Shortcuts

Troubleshooting

Sequence Not Loading

• Ensure only A, G, T, C characters are present
• Check that sequence length is divisible by 3
• Verify file format for FASTA uploads

3D Structure Not Rendering

• Structure prediction requires a valid protein-coding sequence
• Very short sequences (<30 codons) may not fold properly
• Try refreshing if the viewer appears blank

Optimization Not Available

• Ensure you are logged in with approved credentials
• Check that sequence passes all validation checks
• Contact support if you experience access issues

Contact & Support

Email: Servicio@tousysbiotech.com

Last updated: January 2026