optnetaligncpp

Optnetaligncpp aligns protein-protein interaction (PPI) networks to identify orthologous proteins across species by integrating topological and sequence similarity information.

Key Features:

• Multiobjective memetic algorithm: Uses a memetic framework that optimizes multiple objectives concurrently.
• Swap-based local search: Applies swap-based local search to refine candidate alignments.
• Genetic operators: Employs mutation and crossover operations to generate diverse network alignments.
• Pareto-based optimization: Utilizes Pareto dominance to balance trade-offs between objectives.
• Simultaneous topology and sequence optimization: Optimizes topological structure and sequence similarity at the same time.
• Multiple high-quality candidate alignments: Produces multiple candidate alignments in a single run for comparative analysis.
• Alignment diversity characterization: Provides a comprehensive characterization of alignment diversity between two PPI networks.

Scientific Applications:

• Orthology detection: Identifies orthologous proteins across species by integrating topology and sequence information.
• Cross-species PPI comparison: Compares PPI network structure and conserved interactions between species.
• Trade-off analysis: Evaluates compromises between topological accuracy and biological relevance in network alignments.
• Alignment diversity analysis: Assesses the range of plausible alignments for downstream interpretation and validation.
• Algorithm and objective evaluation: Informs design and evaluation criteria for network alignment objectives and benchmarks.

Methodology:

Implements a multiobjective memetic algorithm using swap-based local search plus mutation and crossover operators, and applies Pareto dominance to jointly optimize topological structure and sequence similarity.