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Table 7 Time spent by \(\mathsf {eGSA}\) according to the prefix array size

From: Generalized enhanced suffix array construction in external memory

Dataset

\(p=0\)

\(p=5\)

\(p=10\)

\(p=15\)

\(p=20\)

Time in \(\upmu \)s/byte

 dna.8GB

5.68

4.97

4.91

4.48

5.03

 protein.8GB

2.58

2.00

2.04

2.00

2.12

 gutenberg.8GB

2.33

1.66

1.46

1.48

1.33

 enwiki.8GB

2.25

1.87

1.54

1.64

1.48

Efficiency

 dna.8GB

0.97

0.81

0.93

0.93

0.83

 protein.8GB

0.92

0.87

0.83

0.82

0.76

 gutenberg.8GB

0.92

0.78

0.75

0.69

0.74

 enwiki.8GB

0.92

0.80

0.82

0.70

0.74

  1. The experiment with \(p=10\) is the same presented in Figs.  2, 3, 4 and 5 and \(p=0\) means that the prefix assembly strategy was not used by the algorithm
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Algorithms for Molecular Biology

ISSN: 1748-7188