GASOLINE: a Cytoscape app for multiple local alignment of PPI networks

Giovanni Micale, Andrea Continella, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Abstract

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.
Original languageEnglish
Article number140
JournalF1000Research
Volume3
DOIs
Publication statusPublished - 2014
Externally publishedYes

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