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Table 5 GO MF running time comparisons

From: NetGrep: fast network schema searches in interactomes

   Running time (s)
Topology Query Narada NetMatch NetGrep
Triangle GO:0003677, GO:0004386, GO:0004672   15 0.1
Triangle GO:0004386, GO:0004672, GO:0030528   16 0.2
Triangle GO:0003723, GO:0003723, GO:0003723   15 1.9
Quad GO:0004386, GO:0003677, GO:0016874, GO:0016829 1 14 0.2
Quad GO:0016787, GO:0030234, GO:0005515, GO:0008233 2.3 17 1.2
Quad GO:0003677, GO:0003723, GO:0005515, GO:0005198 4 16 1.9
Quad GO:0016787, GO:0005198, GO:0003677, GO:0016779 2.2 17 1.7
Quad GO:0016787, GO:0016740, GO:0016779, GO:0030528 4.8 16 2.9
Y-star GO:0008233, GO:0016874, GO:0030234, GO:0005215   15 0.2
Y-star GO:0005515, GO:0004721, GO:0008233, GO:0016740   17 0.8
Y-star GO:0005515, GO:0008233, GO:0005198, GO:0005215   17 3.9
Y-star GO:0030528, GO:0005515, GO:0016740, GO:0005215   14 1.5
Y-star GO:0016740, GO:0005515, GO:0030528, GO:0005215   14 5.2
  1. A comparison of running times (in seconds) for several sample schemas annotated with GO molecular function slim terms on the S. cerevisiae interaction network using Narada, NetMatch and NetGrep. Of the previous methods, Narada and NetMatch are chosen as they can be run off-the-shelf for these schemas; note, however, that Narada only handles linear topology queries. All reported running times are for search and output only. In the case of the Y-stars, the first term shown annotates the central node. The schemas shown have between 10 and 11,000 instances in S. cerevisiae.