Table 1.

Algorithm benchmarks

	600k		Chr20
P-value	10−6	10−4	10−6	10−4
MOODS
Naive algorithm	6.5 s	7.3 s	689 s	782 s
Permutated lookahead	3.8 s	6.3 s	405 s	677 s
MLF	0.4 s	1.1 s	16.0 s	117 s
TFBS	20.4 s	53.1 s	–	–
Motility	103 s	103 s	180 min	181 min
Biopython	42 min	41 min	–	–
Matches	952	7.3 × 104	1.1 × 105	6.7 × 106

We used two target sequences: ‘600k’ is a 600 kb long human DNA fragment, and ‘Chr20’ is the 62 Mb long human chromosome 20. The total scanning times for each algorithm or package are given, with ‘–’ indicating that the dataset was too large to be processed. The reported times include the construction of the data structures required in scanning as well as the scanning itself. The ‘matches’ row gives the total number of matches found for each P-value.