GASOLINE

A Cytoscape App for multiple local alignment of protein-protein interaction (PPI) networks
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: http://ferrolab.dmi.unict.it/gasoline/gasoline.html Sample networks, orthology similarity files and GO annotations: http://ferrolab.dmi.unict.it/gasoline/gasoline.html#download

2.0

Works with Cytoscape 3.0

Release Notes

- Use protein names instead of orthology scores when aligning two or more networks defined on the same set of networks; - User-defined density threshold for the aligned complexes; - Automatical detection of the ideal number of iterations of Gibbs sampling for network alignment; - Use of BLAST E-values for computing orthology similarities between proteins of different networks.

1.2

Works with Cytoscape 3.0

Release Notes

- Fixed a bug with Mac Os operating systems: app was recompiled with Java version 6 instead of Java version 7

1.1

Works with Cytoscape 3.0

Release Notes

- Fixed format check on network input files - Fixed format check on orthology files - Fixed format check on GO annotation files

1.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 2.0

Released 2 Feb 2015

Works with Cytoscape 3.0

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CYTOSCAPE 2

Version 1.0

Released 3 Jan 2014

Works with Cytoscape 2.8

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