GASOLINE (Greedy And Stochastic algorithm for Optimal Local Alignment of Interaction NEtworks) is a Cytoscape App for multiple local alignment of protein-protein interaction (PPI) networks. It uses a statistical iterative sampling in connection to a greedy strategy and can produce biologically significant alignments in reasonable running time, even for very large input instances.
GASOLINE can compute and visualize local alignments in a user-friendly way, without requiring postprocessing operations. Alignments can also be analyzed, by annotating proteins with corresponding GO categories, provided as input by the user.
Requires Java 7 and Cytoscape 3.2 or later.
USER DOCUMENTATION for the App:
Sample networks, orthology similarity files and GO annotations: