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Table 4 Comparison of running times for the exact algorithm and the sampling approach. Comparison of running times for the exact algorithm and the sampling approach (1000 samples) on an Intel Xeon 2.8 GHz CPU.(n = sequence length; * computed on an UltraSparc III 900 MHz using 64-bit.)

From: Complete probabilistic analysis of RNA shapes

n

Sampling

Exact Algorithm

57 nt

6.42 s

0.33 s

74 nt

17.36 s

0.93 s

94 nt

69.56 s

31.85 s

108 nt

36.24 s

57.43 s

130* nt

184.85 s

12016.68 s

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BMC Biology

ISSN: 1741-7007

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