GASOLINE

GASOLINE is a Cytoscape app that enables users to efficiently align and compare multiple protein-protein interaction (PPI) networks from distantly related species. The app implements a greedy and stochastic algorithm to identify local alignments between the input networks. The alignment process begins by finding sets of similar nodes, called seeds, then iteratively extends and refines these alignments using a Gibbs sampling strategy.

GASOLINE allows users to visualize the aligned networks within Cytoscape without additional post-processing steps. Furthermore, the app can incorporate Gene Ontology (GO) terms associated with the aligned proteins, facilitating functional analysis of the alignments.

GASOLINE can align multiple large PPI networks within minutes, providing a powerful tool for researchers to discover conserved interaction patterns and gain insights into specific biological functions or processes across different species.