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.

Banks et al. Genome Biology 2008 9:R138   doi:10.1186/gb-2008-9-9-r138