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Bioinformatics Advance Access originally published online on July 24, 2008
Bioinformatics 2008 24(19):2265-2266; doi:10.1093/bioinformatics/btn380
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference

Faruck Morcos 1,*, Charles Lamanna 1, Marcin Sikora 2 and Jesús Izaguirre 1

1Department of Computer Science and Engineering and 2Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA

*To whom correspondence should be addressed.


  Abstract

Summary: Cytoprophet is a software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape, an open source software framework for analysis and visualization of molecular networks. Cytoprophet implements three algorithms that predict new potential physical interactions using the domain composition of proteins and experimental assays. The algorithms for protein and domain interaction inference include maximum likelihood estimation (MLE) using expectation maximization (EM); the set cover approach maximum specificity set cover (MSSC) and the sum-product algorithm (SPA). After accepting an input set of proteins with Uniprot ID/Accession numbers and a selected prediction algorithm, Cytoprophet draws a network of potential interactions with probability scores and GO distances as edge attributes. A network of domain interactions between the domains of the initial protein list can also be generated. Cytoprophet was designed to take advantage of the visual capabilities of Cytoscape and be simple to use. An example of inference in a signaling network of myxobacterium Myxococcus xanthus is presented and available at Cytoprophet's website.

Availability: http://cytoprophet.cse.nd.edu

Contact: cytoprophet{at}cse.nd.edu

Supplementary information: Examples and supplementary data are accessible at http://cytoprophet.cse.nd.edu

Associate Editor: Olga Troyanskaya

Received on May 2, 2008; revised on May 2, 2008; accepted on July 19, 2008

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