A hybrid method for the exact planted (l, d) motif finding problem and its parallelization

BMC Bioinformatics

Table 3 The performance of the HEP_PMSprune(ons) for different values of n and l

n	d	l	*ons*	*T_ons*	*ons_exp*	*T_onsexp*	*T_pms*
300	3	11	9	0.0001	3-20	0.0001	0.0001
600	3	11	10	1.34	10	1.34	1.92
900	3	11	14	4	11-16	4	5
1200	3	11	17	7	17	7	8
1500	3	11	20	16	20	16	16
300	3	12	6	0.05	4-20	0.05	0.05
600	3	12	8	0.83	4-20	0.83	0.83
900	3	12	8	1.5	6-20	1.5	1.5
1200	3	12	9	3	6-15	3	4
1500	3	12	10	5	8-12	5	7
300	4	13	7	3	5-20	3	3
600	4	13	9	24.55	9	24.55	33.95
900	4	13	11	81	11	81	109
1200	4	13	14	190	14	190	217
1500	4	13	17	353	17-19	356	360
300	4	14	6	1	4-20	1	1
600	4	14	7	6.5	7-18	6.5	7
900	4	14	8	21.5	8-9	21.5	24
1200	4	14	8	54	8	54	67
1500	4	14	9	107	9	107	146
300	4	15	5	0.25	4--20	0.25	0.25
600	4	15	5	1.25	4-20	1.25	1.25
900	4	15	6	5	5-20	5	5
1200	4	15	6	12	8	10	13
1500	4	15	7	16.5	7-13	16.5	20
300	4	16+	5	0.002	3-20	0.002	0.002
600	4	16+	5	0.25	4-20	0.25	0.25
900	4	16+	5	1	4-20	1	1
1200	4	16+	6	2.34	5-20	2.34	2.34
1500	4	16+	6-8	4.89	5-20	4.89	4.89
300	5	15	7	38	6-10	38	46
600	5	15	8	361.2	8	360	462
900	5	15	9	1250	9	1250	1847
1200	5	15	11	2976	11	2976	4060
1500	5	15	13	5829	13	5829	6969
300	5	17	5	2	5-20	2	2
600	5	17	6	27	13-20	19	19
900	5	17	5	103	7-20	92	92
1200	5	17	6	231	6-8	224	264
1500	5	17	6	439	6-8	439	552
300	5	18+	5	1	5-20	1	1
600	5	18+	6	5	6-20	4	4
900	5	18+	6-7	14	6-20	14	14
1200	5	18+	6-7	33	6-20	33	33
1500	5	18+	6-8	74	6-20	74	74

The first column includes the sequence length n, the second includes the hamming distance d, and the third includes the motif length l. The entries l+, means greater than l leads to no improvement. 'ons' stands for the theoretically computed q, while "ons_exp" stands for the experimentally found one. We report range of ons_exp that yielded best time. There also range of ons for l+. "T_ons" and "T_ons_exp" stand for the times (in seconds) with ons and ons_exp, respectively. "T_pms" stands for the time with the original PMSprune algorithm only.

ISSN: 1471-2105