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Briefings in Functional Genomics and Proteomics Advance Access published online on April 28, 2008
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/eln015
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© The Author 2008. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

A review on models and algorithms for motif discovery in protein–protein interaction networks

Giovanni Ciriello and Concettina Guerra

Corresponding author. Giovanni Ciriello, Department of Information Engineering, University of Padova Via Gradenigo 6a, 35131 Padova, Italy. Tel: +39 049 827 7928; Fax: +39 049 827 7799; E-mail: ciriello{at}dei.unipd.it

Several algorithms have been recently designed to identify motifs in biological networks, particularly in protein–protein interaction networks. Motifs correspond to repeated modules in the network that may be of biological interest. The approaches proposed in the literature often differ in the definition of a motif, the way the occurrences of a motif are counted and the way their statistical significance is assessed. This has strong implications on the computational complexity of the discovery process and on the type of results that can be expected. This review presents in a systematic way the different computational settings outlining their main features and limitations.

Keywords: network motifs, PPI networks, computational biology, graph mining


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