NetGrep: fast network schema searches in interactomes

Eric Banks¹^,2 , Elena Nabieva¹^,2 , Ryan Peterson¹^,3 and Mona Singh¹^,2

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

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

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

author email corresponding author email

Genome Biology 2008, 9:R138doi:10.1186/gb-2008-9-9-r138


Published:	18 September 2008

Subject areas: Bioinformatics, Genome studies

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.