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Table 2 Methods comparison on simulated datasets.

From: iTriplet, a rule-based nucleic acid sequence motif finder

Models Neighborhood Probability MotifEnumerator RISOTTO PMSprune iTriplet iTriplet (parallel)
11,2 0.7% 6 s 2.2 s 1 s 2 s 1 s
12,3 5.4% 1 m 40 s 4 s 33 s 18 s
13,3 2.4% 2 m 33 s 2 s 6 s 4 s
14,4 11% -a 8 m 1 m 3 m 2 m
15,4 5.6% - 6 m 16 s 36 s 19 s
16,5 19% - 82 m 13.5 m 26 m 13 m
18,6 28% - -b -b 3 h 1.5 h
19,6 18% - - - 27 m 14 m
24,8 23% - - - 4 h 2 h
28,8 3% - - - 19 s 10 s
30,9 5% - - - 2.3 m 1.5 m
38,12 7% - - - 1 h 33 m
40,12 3% - - - 5 m 4 m
  1. Neighborhood probability refers to the probability that two l mers differ by no more than 2d differences. The formula to calculate neighborhood probability is stated in the Additional file 1. Time is measured in seconds (s), minutes (m) or hours (h). (a) MotifEnumerator ran out of memory for l greater than 13. (b) Program took more than 6 hours to handle for the model <18,6> or longer. For the parallel version of iTriplet, reported runtime is the longest lapse time required for all nodes to finish.