Table 2 The comparison of the search efficiency of the Brute Force and Boyer-Moore methods for different lengths of enzyme recognition sequences based on REBASE version 709. Brute Force is presented as “BF”; Boyer-Moore is presented as “BM”
From: REHUNT: a reliable and open source package for restriction enzyme hunting
Enzyme recognition sequence length | Enzyme recognition sequence number | Average elapsed time (ms) | The elapsed time ratio in BF/BM | Average used memory (Mbytes) | The used memory ratio in BF/BM | ||
|---|---|---|---|---|---|---|---|
BF | BM | BF | BM | ||||
1 | 328 | 22.45 | 24.09 | 0.93 | 2.89 | 2.89 | 1.00 |
2 | 3 | 23.00 | 15.33 | 1.50 | 2.89 | 3.75 | 0.77 |
3 | 1 | 24.00 | 0.00 | – | 0.26 | 1.74 | 0.15 |
4 | 641 | 24.03 | 8.80 | 2.73 | 0.26 | 3.59 | 0.07 |
5 | 757 | 24.00 | 7.91 | 3.04 | 0.26 | 2.03 | 0.13 |
6 | 1428 | 24.06 | 6.80 | 3.54 | 0.26 | 1.00 | 0.26 |
7 | 818 | 25.01 | 6.41 | 3.90 | 2.10 | 1.18 | 1.79 |
8 | 64 | 24.95 | 6.39 | 3.90 | 2.10 | 0.53 | 3.95 |
9 | 49 | 24.96 | 7.16 | 3.48 | 2.10 | 4.24 | 0.50 |
10 | 70 | 25.03 | 5.60 | 4.47 | 2.10 | 3.91 | 0.54 |
11 | 129 | 26.08 | 4.66 | 5.60 | 3.85 | 4.17 | 0.92 |
12 | 94 | 25.87 | 4.24 | 6.10 | 3.85 | 3.82 | 1.01 |
13 | 82 | 26.37 | 5.04 | 5.23 | 3.85 | 3.56 | 1.08 |
14 | 40 | 26.20 | 4.28 | 6.13 | 3.85 | 3.31 | 1.16 |
15 | 22 | 27.14 | 3.50 | 7.75 | 1.31 | 3.54 | 0.37 |
16 | 4 | 27.25 | 0.00 | – | 1.31 | 3.29 | 0.40 |
17 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
18 | 3 | 26.67 | 0.00 | – | 1.31 | 2.99 | 0.44 |
19 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
20 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
21 | 1 | 29.00 | 0.00 | – | 3.06 | 2.86 | 1.07 |
22 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
23 | 7 | 28.86 | 5.57 | 5.18 | 0.53 | 3.02 | 0.17 |
24 | 5 | 28.60 | 7.20 | 3.97 | 0.53 | 2.90 | 0.18 |
25 | 6 | 29.17 | 5.33 | 5.47 | 0.53 | 2.77 | 0.19 |
26 | 5 | 29.20 | 9.60 | 3.04 | 0.53 | 2.67 | 0.20 |
27 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
28 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
29 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
30 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
31 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
32 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
33 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |
34 | 1 | 30.00 | 15.00 | 2.00 | 4.11 | 2.43 | 1.69 |
35 | 0 | 0.00 | 0.00 | – | 0.00 | 0.00 | – |