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Genome Biol. 2008;9(9):R138. doi: 10.1186/gb-2008-9-9-r138. Epub 2008 Sep 18.

NetGrep: fast network schema searches in interactomes.

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  • 1Department of Computer Science, Princeton University, Princeton, NJ 08540, USA. ebanks@cs.princeton.edu


NetGrep (http://genomics.princeton.edu/singhlab/netgrep/) 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.

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