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NetGrep: fast network schema searches in interactomes

Eric Banks12, Elena Nabieva12, Ryan Peterson13 and Mona Singh12*

Author Affiliations

1 Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08540, USA

2 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Lab, Princeton, NJ 08544, USA

3 Current address: Department of Computer Science, Cornell University, 4130 Upson Hall, Ithaca, NY 14853, USA

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Genome Biology 2008, 9:R138  doi:10.1186/gb-2008-9-9-r138

Published: 18 September 2008

Abstract

NetGrep (http://genomics.princeton.edu/singhlab/netgrep/ webcite) is a system for searching protein interaction networks for matches to user-supplied 'network schemas'. Each schema consists of descriptions of proteins (for example, their molecular functions or putative domains) along with the desired topology and types of interactions among them. Schemas can thus describe domain-domain interactions, signaling and regulatory pathways, or more complex network patterns. NetGrep provides an advanced graphical interface for specifying schemas and fast algorithms for extracting their matches.