Table 5

GO MF running time comparisons

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

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.

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