Netmatchstar: An enhanced Cytoscape network querying app

Fabio Rinnone; Giovanni Micale; Vincenzo Bonnici; Gary D. Bader; Dennis Shasha; Alfredo Ferro; Alfredo Pulvirenti; Rosalba Giugno

doi:10.12688/f1000research.6656.2

Netmatchstar: An enhanced Cytoscape network querying app

Fabio Rinnone, Giovanni Micale, Vincenzo Bonnici, Gary D. Bader, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno

Research output: Contribution to journal › Article › peer-review

Abstract

We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.

Original language	English (US)
Article number	479
Journal	F1000Research
Volume	4
DOIs	https://doi.org/10.12688/f1000research.6656.2
State	Published - 2015

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology
Pharmacology, Toxicology and Pharmaceutics(all)

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10.12688/f1000research.6656.2

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title = "Netmatchstar: An enhanced Cytoscape network querying app",

abstract = "We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.",

author = "Fabio Rinnone and Giovanni Micale and Vincenzo Bonnici and Bader, {Gary D.} and Dennis Shasha and Alfredo Ferro and Alfredo Pulvirenti and Rosalba Giugno",

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AU - Rinnone, Fabio

AU - Micale, Giovanni

AU - Bonnici, Vincenzo

AU - Bader, Gary D.

AU - Shasha, Dennis

AU - Ferro, Alfredo

AU - Pulvirenti, Alfredo

AU - Giugno, Rosalba

PY - 2015

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AB - We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.

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Netmatchstar: An enhanced Cytoscape network querying app

Abstract

ASJC Scopus subject areas

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