Table 4

Running time comparisons

Running time (s)


Sample query

PathBLAST

Fanmod

Narada

NetMatch

NetGrep


Signaling pathway 1

28

4.2

Signaling pathway 2

26.9

MAPK pathway

90

0.02

Feed-forward motif

32

5.2

1.4

Kinate motif

32

5

0.5

SH3 domain interaction

0.5

ACT1 genetic interaction

15

0.1


Running times (in seconds) for several sample queries on the S. cerevisiae interaction network, using PathBLAST, Fanmod, Narada, NetMatch and NetGrep. All reported running times are for search and output only. As in Table 1, PathBLAST is used as a prototypical example of a network alignment tool and Fanmod represents network motif finders. Note that SAGA is excluded here because it cannot be run on Windows. The sample schemas correspond to those provided in Figure 2, except that two distinct queries are used for Figure 2a. In the first, all three kinases in the pathway are required. In the second, two of the kinases are designated as optional (as in Figure 2a). Each query is run ten times and the average computation time is provided. Row entries are left blank for any tool that is unable to find instances of a particular schema because of feature limitations.

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

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