Graemlin

Graemlin aligns multiple protein interaction networks to identify conserved functional modules and network topologies across species.

Key Features:

• Scalable multiple network alignment: Aligns multiple global protein interaction networks simultaneously for cross-species comparison.
• Explicit functional evolution model: Implements an explicit model of functional evolution that generalizes existing alignment scoring schemes.
• Detection of conserved network topologies: Identifies conserved network topologies beyond traditional protein complexes and metabolic pathways.
• Enhanced sensitivity and scalability: Improves sensitivity and scalability relative to prior methods for processing large, high-density interaction networks.
• Quantitative benchmarking with KEGG: Assesses alignment quality using quantitative benchmarks that compare recovered conserved functional modules to those cataloged in the KEGG database.

Scientific Applications:

• Conserved module identification: Identification of conserved functional modules across species using protein interaction data.
• Evolutionary inference: Inference of evolutionary relationships and functional similarities among proteins and pathways across species.
• Analysis of dense interaction datasets: Analysis of high-density, large-scale protein interaction networks from high-throughput experiments.

Methodology:

Performs global alignment of multiple protein interaction networks using an explicit model of functional evolution and evaluates alignments with quantitative benchmarks against the KEGG database.