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Table 2 Running time of the island method and the deviation in λ

From: Island method for estimating the statistical significance of profile-profile alignment scores

 

m, n= 350

m, n= 1500

Method

2 s

4 s

8 s

16 s

32 s

64 s

WeightedLogOdds

7%

5%

1%

4%

2%

1%

CrossProduct

10%

5%

2%

14%

7%

4%

JensenShannon

8%

4%

2%

4%

3%

2%

Multinomial

6%

3%

3%

5%

2%

1%

  1. The actual running time of the island method and the (percent) difference in the island estimates of λ from the values obtained with the direct method. The results are averaged over 100 pairs of random profiles. The standard error in each estimate of λ for both methods is 0.78%. The running time of the direct method is ~1.3 minutes for comparisons of size 350 × 350 and ~30 minutes for comparisons of size 1500 × 1500.
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BMC Bioinformatics

ISSN: 1471-2105

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