Comparing protein interaction networks can reveal interesting patterns ofinteractions for a specific function or process in distantly related species. In thispaper we present GASOLINE, a Cytoscape app for multiple local alignments ofPPI (protein-protein interaction) networks. The app is based on thehomonymous greedy and stochastic algorithm. GASOLINE starts with theidentification of sets of similar nodes, called seeds of the alignment. Alignmentsare then extended in a greedy manner and finally refined. Both the identificationof seeds and the extension of alignments are performed through an iterativeGibbs sampling strategy. GASOLINE is a Cytoscape app for computing andvisualizing local alignments, without requiring any post-processing operations.GO terms can be easily attached to the aligned proteins for further functionalanalysis of alignments. GASOLINE can perform the alignment task in fewminutes, even for a large number of input networks.

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

GIUGNO, ROSALBA;
2014-01-01

Abstract

Comparing protein interaction networks can reveal interesting patterns ofinteractions for a specific function or process in distantly related species. In thispaper we present GASOLINE, a Cytoscape app for multiple local alignments ofPPI (protein-protein interaction) networks. The app is based on thehomonymous greedy and stochastic algorithm. GASOLINE starts with theidentification of sets of similar nodes, called seeds of the alignment. Alignmentsare then extended in a greedy manner and finally refined. Both the identificationof seeds and the extension of alignments are performed through an iterativeGibbs sampling strategy. GASOLINE is a Cytoscape app for computing andvisualizing local alignments, without requiring any post-processing operations.GO terms can be easily attached to the aligned proteins for further functionalanalysis of alignments. GASOLINE can perform the alignment task in fewminutes, even for a large number of input networks.
2014
Network Aligment
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/940429
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