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Table 4 Performance results Performance results for random RNA sequences and comparison to pknotsRE. The performance of pknotsRG-loc is similar to pknotsRG-mfe and therefore not shown. The bounded version restricts pseudoknots to a maximum length of 150 nucleotides; measured on an UltraSPARC CPU with 450 MHz and 4 GB main memory. Time is measured in (h:m:s), memory in MB.

From: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

Length

pknotsRE

pknotsRG-mfe

pknotsRG-enf

pknotsRG-enf bounded

 

Time

Mem.

Time

Mem.

Time

Mem.

Time

Mem.

40

17.4

-

0.7

1

0.9

2

0.9

2

80

21:11

38

9.5

5

8.7

5

8.8

5

100

1:23:50

80

20.0

8

32.5

10

34.5

9

200

-

-

6:46

36

8:03

42

6:33.6

42

300

-

-

33:07

80

44:58

102

20:48.4

90

400

-

-

1:48:08

146

2:28:18

184

45:28.9

155