|
Application
|
output size
|
standard CGR
|
quadtree CGR
|
Suffix Tree
|
|---|
|
LCE
|
1
|
O(1)
|
O(1)
|
O(1)
|
|
k-mismatch
|
N
|
O(kN)
|
O(kN)
|
O(kN)
|
|
Exact palindromes
|
N
|
O(N)
|
O(N)
|
O(N)
|
|
k-mismatch palindromes
|
N
|
O(kN)
|
O(kN)
|
O(kN)
|
|
Exact tandem repeats
|
z
|
O(N log N + z)
|
O(N log N + z)
|
O(N log N + z)
|
|
k-mismatch tandem repeats
|
z
|
O(kN log N + z)
|
O(kN log N + z)
|
O(kN log N + z)
|
|
Longest common suffix
|
1
|
O(1)
|
O(1)
|
O(1)
|
|
Exact match (MATCHES)
|
occ
|
O(N)
|
O(L + occ)
|
O(L + occ)
|
|
Occurrences (COUNT)
|
1
|
O(N)
|
O(L + occ)
|
O(L + occ)
|
|
Longest common substring
|
1
|
O(N log N)
|
O(N log N)
|
O(N)
|
- This time complexity analysis does not include the pre-processing step of building the required indexes, as all depend solely in the size N of the input string S. In the following L is the length of pattern P.
