Efficient sequential and parallel algorithms for planted motif search

BMC Bioinformatics

Table 3 Runtime comparison between PMS8 and qPMS7 on real datasets from [[20]]

Dataset	n	Total no. bases	l	d	PMS8 time	qPMS7 time
dm01r	4	6000	21	4	1	55
dm01r	4	6000	23	5	1	6
dm04r	4	8000	21	4	1	5
dm04r	4	8000	23	5	1	5
hm01r	18	36000	21	6	10	14
hm01r	18	36000	23	7	25	40
hm02r	9	9000	21	6	1	11
hm02r	9	9000	23	7	4	35
hm03r	10	15000	21	6	3	24
hm03r	10	15000	23	7	14	146
hm04r	13	26000	21	6	6	44
hm04r	13	26000	23	7	15	39
hm05r	3	3000	21	4	1	6
hm05r	3	3000	23	5	1	46
hm08r	15	7500	17	5	1	7
hm08r	15	7500	17	6	46	251
hm19r	5	2500	23	5	1	5
hm19r	5	2500	23	6	1	5
hm20r	35	70000	21	6	27	32
hm20r	35	70000	23	7	56	136
hm26r	9	9000	23	6	1	5
hm26r	9	9000	23	7	5	46
mus02r	9	9000	21	6	1	11
mus02r	9	9000	23	7	2	45
mus04r	7	7000	21	6	1	15
mus04r	7	7000	23	7	2	22
mus05r	4	2000	21	5	1	79
mus05r	4	2000	23	6	1	5
mus07r	4	6000	21	5	1	79
mus07r	4	6000	23	5	1	6
mus10r	13	13000	21	6	2	56
mus10r	13	13000	23	7	2	70
mus11r	12	6000	21	7	8	150
mus11r	12	6000	23	8	23	938
yst01r	9	9000	21	6	2	14
yst01r	9	9000	23	7	8	63
yst02r	4	2000	21	5	1	5
yst02r	4	2000	23	6	1	6
yst03r	8	4000	21	6	1	8
yst03r	8	4000	23	7	1	19
yst04r	6	6000	21	4	1	5
yst04r	6	6000	23	5	1	5
yst05r	3	1500	21	4	1	5
yst05r	3	1500	23	5	1	5
yst06r	7	3500	21	6	1	6
yst06r	7	3500	23	7	2	12
yst08r	11	11000	21	5	1	6
yst08r	11	11000	23	6	1	6
yst09r	16	16000	21	6	2	17
yst09r	16	16000	23	7	6	68

For each dataset we tested two combinations of l and d. For qPMS7 we set q =n. Both algorithms were executed on a single CPU core. Time is reported in seconds, rounded up to the next second.

ISSN: 1471-2105