palAlign

PalAlign: Abstraction-free metabolic pathway alignment algorithm

PalAlign performs pairwise alignment of metabolic pathways by preserving enzymes, reactions, and compounds as distinct entity types and integrating homological similarity with pathway topology.

Key Features:

• Abstraction-Free Alignment: Maintains all biochemical entity types without reducing pathways to simplified graph models.
• Entity-Specific Alignment: Aligns enzymes, reactions, and compounds using pairwise homology and topological organization.
• Eigenvalue-Based Algorithm: Formulates and solves an eigenvalue problem for each entity type to compute alignments.
• Reachability Set Integration: Ensures cross-entity consistency by incorporating reachability sets during alignment integration.

Scientific Applications:

• Comparative Pathway Analysis: Identifies functional similarities between metabolic pathways by integrating homological and topological information across entity types.

Methodology:

Solves the pairwise pathway alignment problem without abstraction by combining homological similarity and topological structure, applying eigenvalue-based optimization per entity type and integrating results through reachability sets.