Categories: graph analysis, network alignment, network analysis, network comparison

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. WEB SITE: https://alpha.dmi.unict.it/~gmicale/gasoline/ USER DOCUMENTATION for the App: https://alpha.dmi.unict.it/~gmicale/gasoline/Files/Documentation_GASOLINE.pdf SAMPLE DATASETS AND ORTHOLOGY SIMILARITY FILES: https://alpha.dmi.unict.it/~gmicale/gasoline/#download

Authors:

• Giovanni Micale (University Of Catania)
• Andrea Continella (Polytechnic University of Milan)
• Alfredo Pulvirenti (University Of Catania)
• Rosalba Giugno (University Of Verona)
• Alfredo Ferro (University Of Catania)