Modelling the impact of DNA sequence repeats on gene inversions and gene-strand bias in bacteria

A computational model simulating how DNA sequence repeats influence gene inversions and strand bias in bacterial genomes.

Abstract

This project investigates how different DNA repeat configurations (direct, inter-inverted, intra-inverted) affect gene-strand bias through inversion events. The model demonstrates:

• Null Model Behavior: Without selection pressure, gene-strand bias stabilizes at 50-50 distribution
• Selection Impact: Imposing constraints through inversion disparity scores maintains existing strand bias
• Evolutionary Insights: Provides framework for understanding bacterial adaptation through chromosomal rearrangements

Key Features

• Circular bacterial genome simulation with configurable parameters:
  • Ori/Ter positions
  • Repeat distributions (direct, inter/intra-inverted)
  • Gene allocation between strands
• Two operational modes:
  • Null Model: Unconstrained inversions
  • Selection Model:
    • Gene count imbalance thresholds
    • Inversion Disparity Score (IDS) calculations
    • Penalty limit constraints
• Analytical tools for:
  • Strand bias quantification
  • Inversion event tracking
  • Fitness impact assessment

Key Configurable Parameters (via config.yaml):

• inversion_disparity_limit: 10/25/no-limit
• repeat_distribution: Random/Clustered
• fitness_function: Normal/Exponential distribution

Results Interpretation

Null Model Dynamics

• Rapid convergence to 50-50 strand distribution
• Demonstrates baseline evolutionary pressure from unconstrained inversions

Selection Model Outcomes (Figs 5-7)

Penalty Limit	Strand Bias Stability	Inversion Frequency
10	High	Low
25	Moderate	Medium
no-limit	Low	High

Critical Finding: Higher penalty limits permit larger inversions while maintaining ancestral strand bias patterns

Future Directions

Planned model extensions:

1. GC skewness integration
2. Transcription-replication collision modeling
3. Horizontal gene transfer simulations

License

MIT License - see LICENSE for details.