PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets

Table 3

Site-level identification accuracy on the first group of simulated data sets.

		PairMotifChIP	MEME-ChIP	F-motif	PairMotif+
9	0.2	0.942	0.866	0.942	0.942
	0.5	0.902	0.734	0.902	0.902
	0.8	0.907		0.907	0.907
15	0.2	0.995	0.960	0.995	0.995
	0.5	0.969	0.916	0.969	0.969
	0.8	0.936		0.936	0.936
21	0.2	1.000	0.947	—	—
	0.5	0.988	0.953	—	—
	0.8	0.981	0.844	—	—

Note. —: the result is not obtained because the running time is over 24 hours; the result is not obtained because motif sites are not provided by MEME-ChIP on the corresponding data sets. The site-level identification accuracy is evaluated by the site-level performance coefficient sPC. Since qPMS9 and F-motif report the same motifs and have the same identification accuracy, the results of qPMS9 are not listed in this table.