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Table 4 Results of empirical tests of memory and CPU time required by CM structural alignment algorithms on six known structural RNAs of various sizes.

From: A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

  tRNA 5S rRNA SRP RNA RNase P SSU rRNA LSU rRNA
# of consensus columns 72 116 301 379 1545 2898
# of consensus base pairs 21 35 89 113 462 794
# of consensus unpaired 30 46 123 153 621 1310
CM states (M) 230 357 927 1176 4789 9023
bifurcations (B) 2 1 4 7 30 65
Maximum extra decks needed 1 1 2 2 3 5
Example sequence length (N) 73 120 300 377 1542 2904
Full CYK RAM (MB) 2.6 10.7 168.9 336.7 22705.0 151349.7
Divide & conquer RAM (MB) 0.1 0.4 2.4 3.7 66.8 270.9
Full CYK CPU time (sec) 0.2 0.7 12.7 28.6 n.d. n.d.
CYK CPU time, no trace (sec) 0.1 0.6 10.4 23.8 2614.8 25151.2
Divide & conquer time (sec) 0.2 0.9 22.8 37.8 3594.4 31649.4