Proteny

Proteny detects and analyzes protein-level synteny between diverged genomes to characterize conserved gene order and genomic rearrangements in microorganisms.

Key Features:

• Amino Acid Sequence Analysis: Operates at the amino acid sequence level, providing robustness to codon usage variation when detecting homology.
• Exon Clustering: Clusters groups of exons irrespective of their order to accommodate rearrangements and exon shuffling.
• Statistical Significance: Assigns statistical significance to syntenic clusters to enable selection based on rigorous criteria.
• Visualization Capabilities: Provides visualization methods for synteny analysis at multiple scales.

Scientific Applications:

• Cross-divergence Synteny Analysis: Applied to both closely related and distantly related genomes, including two strains of Aspergillus niger (closely related) and two species of Basidiomycota (distantly related).
• Comparative Benchmarking: Identifies clusters with more true homologies while reducing the number of gene-poor clusters relative to other tools.
• Genomic Variation Studies: Used to study genome rearrangements, assembly errors, gene duplications, and conservation of specific genes.
• Evolutionary and Structural Genomics: Supports investigations of evolutionary relationships and genomic architecture through protein-level synteny evidence.

Methodology:

Analyzes amino acid sequences to detect synteny, clusters exons without regard to order, and assigns statistical significance to identified clusters.