GASOLINE (Greedy and Stochastic Algorithm for Optimal Local alignment of Interaction Networks) is an algorithm for multiple local network alignment based on statistical iterative sampling in connection to a greedy strategy. GASOLINE can produce biologically significant alignments in reasonable running time, even for very large input instances.

Before downloading, be sure to have Java installed. The sources are available upon request. To run the GASOLINE Cytoscape plugin you need to install Cytoscape.

Test Datasets

PPI networks taken from STRING database considering only experimentally verified interactions between proteins.

Pairwise similarity scores between the 6 eukaryotic PPI networks (human, mouse, rat, fly, yeast and worm). Pairwise scores have BLAST E-value > 10e-5.
Orthologies 6

GO annotations (components, functions and processes) for all the proteins of 28 PPI networks. GO annotations are taken from BioDbNet.

Experimental results

Complexes returned by GASOLINE and NetworkBlast-M for the alignment of 6 eukaryotic PPI networks (human, mouse, rat, fly, yeast, worm).
Alignment 6

Complexes returned by GASOLINE for the alignment of 25 vertebrata PPI networks.
Alignment 25

User Manual

To run GASOLINE as stand-alone application please refear to the file README.txt contained in the archive

To run GASOLINE as a cytoscape plugin, you can dowonload the following user guide
Download PDF

If you use GASOLINE for reasearch purpose, please cite the following papers:

  • Micale G, Pulvirenti A, Giugno R, Ferro A (2014). GASOLINE: a Greedy And Stochastic algorithm for Optimal Local multiple alignment of Interaction NEtworks. PLoS ONE 9(6): e98750. doi: 10.1371/journal.pone.0098750 (link)

  • Micale G, Continella A, Ferro A, Giugno R, Pulvirenti A (2014). GASOLINE: a Cytoscape app for multiple local alignment of PPI networks [v2; ref status: indexed,]. F1000Research 3(140), doi:10.12688/f1000research.4537.2 (link)


Giovanni Micale
Dept. of Clinical and Experimental Medicine
University of Catania
Alfredo Pulvirenti
Dept. of Clinical and Experimental Medicine
University of Catania
Rosalba Giugno
Dept. of Computer Science
University of Verona
Alfredo Ferro
Dept. of Clinical and Experimental Medicine
University of Catania


If you have any trouble with the software, you want to report any bug or you need the source code, please contact: and