Efficient computation of spaced seeds

BMC Research Notes

Table 2 Comparison of hill climbing algorithms

w	N	p	k	[ℓ₁..ℓ_k]	HC	Fast HC
11	64	.70	16	[14..27]	7.79	1.24
22	50	.85	10	[25..37]	10.79	1.35
28	100	.90	8	[36..56]	39.83	3.64
28	150	.90	8	[39..63]	69.14	5.86
28	200	.90	8	[41..70]	108.74	8.49
28	100	.90	16	[33..59]	471.51	41.42
28	150	.90	16	[36..66]	788.79	62.50
28	200	.90	16	[39..72]	1075.10	79.51

Speed comparison between the existing (HC) and the new implementation (Fast HC) of the hill climbing heuristic. Several sets of parameters are used. The times (in seconds) are given for a single multiple spaced seed with the given parameters. Fast HC is up to 13.5 times faster than HS. Also, the improvement increases with the size of the input.

ISSN: 1756-0500