Software
NetGrep: fast network schema searches in interactomes
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* Corresponding author: Mona Singh msingh@princeton.edu
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
Genome Biology 2008, 9:R138 doi:10.1186/gb-2008-9-9-r138
Published: 18 September 2008Abstract
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.