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Table 9 Run time, in HH:mm:ss, for random sequences using our Java implementations on our Xeon E5 platform

From: Cache and energy efficient algorithms for Nussinov’s RNA Folding

SeqLength

Classical

Transpose

ByRow

ByBox

RvsC

RvsT

BvsC

BvsT

4000

0:01:29

0:00:49

0:00:49

0:00:13

45.18%

1.62%

85.72%

74.37%

8000

0:14:38

0:06:34

0:06:29

0:01:38

55.70%

1.30%

88.86%

75.17%

12,000

0:46:36

0:21:44

0:21:37

0:05:36

53.60%

0.55%

87.98%

74.23%

16,000

1:56:26

0:51:22

0:51:22

0:13:16

55.88%

-0.02%

88.60%

74.16%

20,000

3:39:36

1:40:09

1:40:05

0:26:10

54.42%

0.06%

88.08%

73.87%

24,000

6:29:22

2:52:43

2:52:54

0:44:43

55.59%

-0.11%

88.52%

74.11%

28,000

8:05:15

4:33:21

4:35:04

1:10:48

43.32%

-0.62%

85.41%

74.10%