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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