UniMoG

UniMoG computes pairwise genome rearrangement distances using five genome rearrangement models (double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion-only, and translocation-only) by representing genomes as sequences of oriented common blocks.

Key Features:

• Supported models: Implements five genome rearrangement models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion-only, and translocation-only.
• Genome representation: Represents genomes as sequences of oriented common blocks for rearrangement analysis.
• Unified framework: Integrates the models through a DCJ-based unified framework.
• Algorithms: Leverages the most efficient existing algorithms for each distance and sorting problem.
• Pairwise distances and sorting scenarios: Computes pairwise distances and generates corresponding optimal sorting scenarios.
• Multi-genome analysis: Supports analysis of an arbitrary number of genomes.
• Output formats: Produces textual and graphical outputs to visualize genome rearrangement operations.

Scientific Applications:

• Comparative genomics: Quantifies pairwise rearrangement distances for comparative analysis of multiple genomes.
• Genome evolution studies: Infers rearrangement-based relationships and histories using computed distances and sorting scenarios.
• Structural variation analysis: Analyzes inversions, translocations, and other rearrangements via model-specific distance measures.
• Model comparison: Enables comparison of outcomes across DCJ, restricted DCJ, HP, inversion-only, and translocation-only models.

Methodology:

Genomes are represented as sequences of oriented common blocks and analyzed within a DCJ-based unified framework; the software applies existing efficient algorithms for each distance and sorting problem to compute pairwise distances and generate optimal sorting scenarios under the five supported models.