GASOLINE

GASOLINE performs multiple local alignments of protein-protein interaction (PPI) networks to compare interaction patterns across species.

Key Features:

• Multiple local alignments: Computes local alignments of multiple PPI networks to identify conserved interaction regions.
• Greedy and stochastic algorithm: Uses a greedy approach combined with stochastic strategies for alignment construction.
• Gibbs sampling refinement: Applies iterative Gibbs sampling to refine both seed identification and alignment extension.
• Seed identification: Identifies similar nodes within PPI networks as initial "seeds" for alignments.
• Gene Ontology annotation: Attaches Gene Ontology (GO) terms to aligned proteins to support functional analysis.
• Cytoscape integration: Implemented as a Cytoscape application for execution within the Cytoscape environment.
• No post-processing required: Produces alignments without the need for additional post-processing steps.
• Performance optimization: Optimized to process a large number of input networks in a short time.

Scientific Applications:

• Comparative network analysis: Enables comparison of PPI networks across different species to detect conserved interactions.
• Functional module discovery: Reveals interaction patterns related to specific biological functions or processes.
• Functional annotation transfer: Facilitates transfer and analysis of Gene Ontology (GO) annotations among aligned proteins.
• Large-scale comparative studies: Supports rapid, comprehensive analysis of many PPI networks for cross-species investigations.

Methodology:

GASOLINE identifies similar nodes as seeds, constructs alignments greedily, and refines seed identification and alignment extension using iterative Gibbs sampling within a stochastic framework.