Genome Synteny Module
Comparative genomic analysis and synteny visualization
Module Overview
The Genome Synteny module provides comprehensive comparative genomic analysis and synteny visualization capabilities. This module serves as the central hub for exploring genomic conservation, evolutionary relationships, and structural variations between different insect species.
Key Features
- 1Filter and select two target species for comprehensive genome synteny analysis
- 2Choose specific chromosomes from each species for detailed comparative analysis
- 3Interact with and edit synteny visualization results for comprehensive analysis
Species Selection for Synteny Analysis
Dual Species Filtering
Select two target species from the comprehensive InsectBase database for comparative genomic synteny analysis.
Selection Criteria
- Species Compatibility: Choose species with comparable genome assemblies
- Evolutionary Distance: Select species with appropriate evolutionary relationships
- Genome Quality: Ensure both species have high-quality genome assemblies
- Annotation Status: Verify both genomes have comprehensive gene annotations
Chromosome Selection
Chromosome Pairing
Select specific chromosomes from each species for detailed comparative synteny analysis and visualization.
Selection Options
- • Browse available chromosomes
- • View chromosome characteristics
- • Check synteny potential
- • Preview analysis scope
Analysis Features
- • Homologous region detection
- • Synteny block identification
- • Inversion and translocation detection
- • Conservation scoring
Synteny Visualization and Editing
Interactive Visualization
Manipulate and edit synteny analysis results through interactive visualization tools for comprehensive comparative genomic analysis.
Visualization Controls
Navigation
- • Zoom in/out for detailed view
- • Pan across chromosome regions
- • Jump to specific coordinates
- • Reset to full view
Editing Tools
- • Adjust synteny block parameters
- • Modify visualization settings
- • Filter results by criteria
- • Export customized views
Synteny Analysis Types
Macrosynteny
- • Whole chromosome comparisons
- • Large-scale rearrangements
- • Chromosome fusion/fission events
- • Evolutionary relationships
Microsynteny
- • Gene order conservation
- • Local rearrangements
- • Gene cluster analysis
- • Functional conservation
Structural Variants
- • Inversions and translocations
- • Duplications and deletions
- • Insertion sites
- • Breakpoint analysis
Analysis Tips for Optimal Results
Species Selection
- Choose species with similar genome sizes for better comparison
- Consider evolutionary distance for meaningful synteny analysis
- Verify both species have high-quality genome assemblies
- Check annotation completeness for accurate gene comparisons
Visualization Optimization
- Start with overview to identify major synteny blocks
- Zoom in for detailed microsynteny analysis
- Adjust color schemes for better contrast
- Use filtering options to focus on specific regions
Usage Examples
Example 1: Drosophila Species Comparison
- Select “Drosophila melanogaster” and “Drosophila simulans” as target species
- Choose corresponding chromosome arms (e.g., 2L vs 2L)
- Run synteny analysis to identify conserved regions
- Zoom in to examine gene order conservation
- Export results for further analysis
Example 2: Cross-Order Comparison
- Select species from different orders (e.g., Diptera vs Lepidoptera)
- Choose chromosomes with similar gene content
- Analyze large-scale rearrangements and inversions
- Identify conserved gene clusters
- Compare structural evolution patterns
Available Data Types
Synteny Blocks
Conserved regions
Gene Alignments
Homologous genes
Rearrangements
Structural variants
Visualizations
Interactive plots