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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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.
AbstractList 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.
Author Ferro, Alfredo
Giugno, Rosalba
Pulvirenti, Alfredo
Micale, Giovanni
Continella, Andrea
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  fullname: Micale, Giovanni
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  organization: Department of Computer Science, University of Pisa, Pisa, 56127, Italy
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  surname: Continella
  fullname: Continella, Andrea
  organization: Department of Electronics, Information and Bioengineering, Polytechnic University of Milan, Milan, 20133, Italy
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  givenname: Alfredo
  surname: Ferro
  fullname: Ferro, Alfredo
  organization: Department of Clinical and Molecular Biomedicine, University of Catania, Catania, 95125, Italy
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  surname: Giugno
  fullname: Giugno, Rosalba
  organization: Department of Clinical and Molecular Biomedicine, University of Catania, Catania, 95125, Italy
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  surname: Pulvirenti
  fullname: Pulvirenti, Alfredo
  email: apulvirenti@dmi.unict.it
  organization: Department of Clinical and Molecular Biomedicine, University of Catania, Catania, 95125, Italy
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– notice: Copyright: © 2014 Micale G et al. 2014
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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.
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SubjectTerms Accuracy
Algorithms
Bioinformatics
Gasoline
Gene expression
Ontology
Protein interaction
Proteins
Software Tool
Stochasticity
Visualization
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Title GASOLINE: a Cytoscape app for multiple local alignment of PPI networks [version 2; peer review: 2 approved, 1 approved with reservations]
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https://www.proquest.com/docview/2623270045
https://search.proquest.com/docview/1613940589
https://pubmed.ncbi.nlm.nih.gov/PMC4197741
https://doaj.org/article/5060eff66eb148079e98d429232126d7
Volume 3
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