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Table 3 Run time for amino acid locate() and count() functions

From: An optimized FM-index library for nucleotide and amino acid search

Amino acid search

Count() Time (s)

Locate() Time (s)

Query length

Hits/query

SeqAn3

AWFM

Speed-up

SeqAn3

AWFM

Speed-up

10

1.00

4.58

.81

5.66

6.40

1.63

3.92

9

1.00

3.91

.83

4.71

5.97

1.38

4.33

8

1.02

3.39

.60

5.69

5.29

1.46

3.61

7

1.47

2.89

.43

6.77

5.41

1.61

3.36

6

9.00

2.38

.38

6.27

15.35

5.52

2.78

5

137.70

1.81

.08

21.95

167.56

73.42

2.28

4

2339.23

0.49

0.30

1.62

1950.45

904.28

2.16

  1. A 200 million character-long simulated target amino acid sequence was indexed with a suffix array sampling ratio of 4. One million length-k amino acid query sequences were sampled from the target, for several values of k
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Algorithms for Molecular Biology

ISSN: 1748-7188