Efficient computation of spaced seeds

BMC Research Notes

Table 1 Comparison of overlap complexity computation algorithms

w	ℓ	OC	Fast OC	VFast OC
9	15	0.012	0.004	0.004
10	17	0.064	0.028	0.024
11	18	0.116	0.048	0.044
12	19	0.204	0.084	0.072
13	20	0.340	0.136	0.116
14	21	0.564	0.208	0.184
15	23	2.792	0.948	0.828
16	24	4.564	1.484	1.300
17	25	7.276	2.648	1.992
18	26	11.368	3.968	2.984

Speed comparison between the existing and the new implementations of the overlap complexity function. Seeds of optimal length for weights between 9 and 18 are considered. In each case, the time (in seconds) is given for the computation of overlap complexity for all $(\begin{matrix} ℓ \\ w \end{matrix})$ seeds with the given parameters. The VFast OC algorithm is the fastest (times in bold), up to 3.8 times faster than the original OC algorithm.

ISSN: 1756-0500