GASOLINE: a Cytoscape app for multiple local alignment of PPI networks [version 2; peer review: 2 approved, 1 approved with reservations]

Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on...

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Published inF1000 research Vol. 3; p. 140
Main Authors Micale, Giovanni, Continella, Andrea, Ferro, Alfredo, Giugno, Rosalba, Pulvirenti, Alfredo
Format Journal Article
LanguageEnglish
Published London Faculty of 1000 Ltd 01.01.2014
F1000Research
F1000 Research Ltd
Subjects
Accuracy
Algorithms
Bioinformatics
Gasoline
Gene expression
Ontology
Protein interaction
Proteins
Software Tool
Stochasticity
Visualization
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Summary:Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithm. GASOLINE starts with the identification of sets of similar nodes, called seeds of the alignment. Alignments are then extended in a greedy manner and finally refined. Both the identification of seeds and the extension of alignments are performed through an iterative Gibbs sampling strategy. GASOLINE is a Cytoscape app for computing and visualizing local alignments, without requiring any post-processing operations. GO terms can be easily attached to the aligned proteins for further functional analysis of alignments. GASOLINE can perform the alignment task in few minutes, even for a large number of input networks.
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GM and AP conceived the project. GM and AC designed the architecture of Cytoscape plugin for previous versions of Cytoscape (up to version 2.8). AC wrote a first implementation of the plugin. GM enabled the porting of the code to the new versions of Cytoscape (from version 3.0 onward) and extended the functionality of the application. AP, RG and AF coordinated the project. GM, AP, RG and AF wrote the paper.
Competing interests: No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.4537.2