NetGrep: fast network schema searches in interactomes

Table 1 Feature comparisons

Feature	PathBLAST [37]	Fanmod [41]	Narada [45]	SAGA [27]	NetMatch [26]	NetGrep
Non-linear queries	X	X		X	X	X
Allows arbitrary protein annotations		1 per node			Unlimited	Unlimited
Boolean combination of annotations				X		X
Inexact matches	X			X		X
Multiple edge types in a network		X			X	X
Boolean combination of edge types						X
UI for searching/choosing annotations			X			X
Can be used with Cytoscape					X	X
Can be used as a standalone	X	X	X	X		X
Custom data sets provided	X			X		X

A comparison of built-in features available in systems that can, in principle, be used for querying interactomes using network schemas. A network alignment tool, PathBLAST, and a network motif finder, Fanmod, are shown for comparison. All other systems are explicitly designed for querying interactomes utilizing labeled subgraphs.

ISSN: 1474-760X