HERA

1. Understanding the Visualization

1.1. Main Components

The HERA visualization consists of several concentric rings, each representing different types of genomic data:

• Reference Backbone: The innermost thin circle representing the reference genome's physical structure with position markers showing base pair coordinates.
• Reference Ring: The blue ring containing annotated features from your GenBank file (genes, proteins, regulatory elements). Click on "others" in the Annotations legend to control visibility.
• Additional Analysis Tracks: Inner colored rings (black, green, purple) showing optional analyses like GC Content and GC Skew.
• Query Rings: Orange rings representing your submitted FASTA sequences. Each query gets its own ring, shown in the "Samples" legend. Each of the query rings contains BLAST Alignment Segments , indicating regions of similarity. The opacity reflects alignment quality based on percent of identity.
• Feature Labels: Text labels around the perimeter showing gene names, protein products, or other annotations from your reference file.

1.2. Color Coding System

The opacity level of BLAST alignment segments directly corresponds to the percent identity score. This visual encoding allows you to quickly identify high-quality alignments (dark, opaque) versus more distant relationships (light, transparent).

2. Control Panels

The left-side control panel provides comprehensive customization through two main sections: HERA Controls and Tracks Data.

2.1. HERA Controls

Identity Thresholds (%)

Define how alignment quality is categorized and displayed:

• Max (default: 70): Upper threshold for high-quality matches
• Middle (default: 50): Mid-range similarity cutoff
• Min (default: 30): Minimum similarity to display

Coverage Threshold (%)

Min (default: 0): Set minimum query coverage required to display an alignment. This filters out partial or short alignments that may be spurious. Higher values show only alignments that cover a substantial portion of the query sequence.

Ring Collapse

Control how features are organized within rings:

• None: Display all features in a single layer (may overlap)
• Strand: Separate forward and reverse strand alignments into different layers

This setting prevents visual overlap and improves clarity when many features align to the same genomic region.

3. Interactive Legends

HERA provides three interactive legends that are automatically generated and update dynamically based on your data and settings.

3.1. Identity Thresholds Legend

Shows the color-opacity gradient used to represent alignment quality. The base color can be customized in the Export tab under "Legends" settings. This legend uses opacity levels to distinguish between different identity ranges.

3.2. Samples Legend

Lists all query sequences (your FASTA submissions) with their assigned colors. Each sample is represented by:

• A colored square (swatch) matching the ring color
• The sample name (from your FASTA file)

3.3. Annotations Legend (Reference Feature Groups)

Displays categories of reference genome features. By default, all features are grouped as "others" (shown in blue). You can create custom groups to organize and color-code features by function:

• GC Skew: Shows GC compositional bias
• GC Content: Overall GC percentage
• AMR Genes: Antimicrobial resistance genes
• Colicin Genes: Colicin-related features
• others: All ungrouped annotation features

Create custom groups in the Tracks Data → Annotations → Add Groups tab to highlight specific gene categories (e.g., "Mobile Elements", "Virulence Factors", "Replication").

4. Tracks Data Panel

The bottom control panel provides detailed management of individual rings and features through two tabs.

4.1. Samples Tab

View and manage all query sequence rings with a sortable, interactive table.

Use the search box to filter specific samples by name. Adjust "entries per page" to show 5, 10, 15, or All entries for easier navigation when working with many samples.

4.2. Annotations Tab

Browse and control individual annotation features from your reference genome.

Features Table

Displays all annotation features with the following columns:

• Feature Name: Gene/protein identifier (based on selected qualifier in HERA Controls → Annotations tab)
• Label Visible: Toggle individual feature labels on/off using checkboxes
• Groups: Shows assigned functional groups (comma-separated if feature belongs to multiple groups)

Add Groups Table

Create custom functional groupings of annotation features to organize and color-code related genes.

Managing Groups

• Change group colors: Click the color swatch in the Annotations legend to open color picker
• Remove groups: Select features, enter group name, click Remove Group
• Multiple groups: Features can belong to multiple groups; most recent group determines display color
• Removing groups: Doesn't delete features, only removes the group association

5. Exporting and Loading Results

HERA provides comprehensive export capabilities through the Export tab in the Control Panel.

5.1. Save Progress

Create a snapshot of your entire session including all customizations, colors, positions, and settings:

• Click Save on Server to store remotely (confirmation message appears)

Click Download Progress to save a .zip file locally containing:

• CGView visualization data (JSON format)
• Session settings (thresholds, styles, positions)
• BLAST alignment results

File name format: {job_id}_HERAproject.zip

5.2. Load Saved Project

1. Go to HERA results tab
2. Upload your _HERAproject.zip file or insert the jobID
3. Click "Load Project" option
4. Visualization reappears with all customizations intact

5.3. Export Images

Generate publication-quality figures in multiple formats with precise control over dimensions and appearance.

Image Area Selection

• Complete Image: Entire visualization including all legends and labels
• Custom: Define specific region using crop controls (Left, Right, Top, Bottom margins)

Background Options

• Transparent: PNG with no background (ideal for overlays in presentations)
• Colored: Select custom background color (white for publications, colored for presentations)

Dimensions & Resolution

Choose units and set precise dimensions:

• Pixels (px): Digital screen resolution
• Centimeters (cm): Print dimensions with DPI calculation
• Inches (in): Print dimensions with DPI calculation

DPI (Dots Per Inch) recommendations:

• 72 dpi: Screen display
• 150 dpi: Draft print quality
• 300 dpi: Publication quality (journals)
• 600 dpi: High-resolution print

File Formats

• PNG: Lossless quality, supports transparency, best for figures
• JPEG: Smaller file size, no transparency, good for presentations
• SVG: Vector format, infinitely scalable, ideal for publications requiring editing

Image Preview

Real-time preview window shows exactly how your exported image will look. Preview updates automatically 400ms after you stop adjusting settings (debounced to prevent lag).

Export Process

1. Configure all settings (area, background, dimensions, format)
2. Review the preview window
3. Enter filename (default: "HERA_image")
4. Click Save Image
5. File downloads automatically with chosen settings

Quick Reference: Common Tasks