Table 1 Comparisons of time complexity among existing string matching methods
From: REHUNT: a reliable and open source package for restriction enzyme hunting
String matching method | Preprocessing time | String matching time |
|---|---|---|
Bitap | Θ(m + k) | O(mn) |
BNDM | O(m) | O(n) |
BOM | O(m) | O(n) |
Boyer-Moore | Θ(m + k) | Best: Ω(n/m) Worst: O(mn) |
KMP | Θ(m) | Θ(n) |
Naïve | 0 | Θ(nm) |
Rabin-Karp | Θ(m) | Average: Θ(n + m) Worst: Θ((n − m)m) |