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.

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

Eddy BMC Bioinformatics 2002 3:18   doi:10.1186/1471-2105-3-18