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

Table 2

Running time on the first group of simulated data sets.

		PairMotifChIP	MEME-ChIP	F-motif	PairMotif+	qPMS9
9	0.2	26.3 s	1510.1 s	9.2 s	300.7 s	247.4 s
	0.5	21.3 s	1507.1 s	9.2 s	212.9 s	234.7 s
	0.8	18.7 s	1462.6 s	9.1 s	217.9 s	226.0 s
15	0.2	35.9 s	1325.0 s	16655.1 s	73048.5 s	—
	0.5	25.6 s	1354.9 s	16403.4 s	23549.0 s	—
	0.8	19.5 s	1466.7 s	15982.7 s	845.6 s	—
21	0.2	47.4 s	1425.5 s	—	—	—
	0.5	30.7 s	1148.5 s	—	—	—
	0.8	20.5 s	1349.2 s	—	—	—

Note. s: seconds; —: over 24 hours.