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Table 2 Run time for nucleotide locate() and count() function.

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

Nucleotide search

Count() Time (s)

Locate() Time (s)

Query length

Hits/query

SeqAn3

AWFM

Speed-up

SeqAn3

AWFM

Speed-up

20

1.00

4.51

1.15

3.12

6.14

2.37

2.60

18

1.01

3.96

.97

4.07

6.93

1.72

4.04

16

1.23

3.50

1.06

3.29

5.21

2.57

2.02

14

4.73

2.90

.76

3.80

8.61

3.67

2.34

12

60.60

2.85

.18

15.85

42.46

29.65

1.43

11

239.40

1.87

.99

1.90

147.54

106.51

1.39

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

ISSN: 1748-7188