Skip to main content

Table 1 Feature comparisons

From: NetGrep: fast network schema searches in interactomes

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
  1. 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.