Suffix Trees

String any sequence of characters.

Substring of string S string composed of
characters i through j, i <= j of S.
S = cater => ate is a substring.
car is not a substring.
Empty string is a substring of S.

Subsequence
Subsequence of string S string composed
of characters i1 < i2 < < ik of S.
S = cater => ate is a subsequence.
car is a subsequence.
The empty string is a subsequence.

String/Pattern Matching
You are given a source string S.
Answer queries of the form: is the string pi a
substring of S?
Knuth-Morris-Pratt (KMP) string matching.
O(|S| + | pi |) time per query.
O(n|S| + Si | pi |) time for n queries.

Suffix tree solution.

O(|S| + Si | pi |) time for n queries.

String/Pattern Matching
KMP preprocesses the query string pi,
whereas the suffix tree method preprocesses
the source string S.
An application of string matching.

Genome project.
Databank of strings (gene sequences).
Character set is ATGF.
Determine if a new sequence is a substring of
a databank sequence.

Definition Of Suffix Tree

Compressed trie with edge information.
Keys are the nonempty suffixes of a given
string S.
Nonempty suffixes of S = sleeper are:

sleeper
leeper
eeper
eper
per, er, and r.

String Matching & Suffixes

pi is a substring of S iff pi is a prefix of some
suffix of S.
Nonempty suffixes of S = sleeper are:

sleeper
leeper
eeper
eper
per, er, and r.

Which of these are substrings of S?

leep, eepe, pe, leap, peel

Last Character Of S Repeats

When the last character of S appears more
than once in S, S has at least one suffix that
is a proper prefix of another suffix.
S = creeper
creeper, reeper, eeper, eper, per, er, r

When the last character of S appears more

than once in S, use an end of string
character # to overcome this problem.
S = creeper#
creeper#, reeper#, eeper#, eper#, per#, er#, r#, #

Suffix Tree For S = abbbabbbb#

1

abbb

5
abbbb#

b#

2
abbbb#

abbbb#
abbbb#

#
3
#

b
b

4
#

b#

Suffix Tree For S = abbbabbbb#

1

abbb

5
abbbb#

2
abbbb#

b#

abbbb#
3

abbbabbbb#
12345678910

abbbb#

#
3
#

b
b

4
#

10

9
8

b#
6

Suffix Tree For S = abbbabbbb#

1

1
abbb

5
1
abbbb#

abbbb#

b#

abbbb#
3

abbbabbbb#
12345678910

b
8
2

abbbb#

#
3
#
b

4
#

10

9
8

b#
6

Suffix Tree Construction

See Web write up for algorithm.
Time complexity

|S| = n, alphabet size = r.

O(nr) using array nodes.
This is O(n) for r a constant (or r <= c).
O(n) expected time using a hash table.
O(n) time algorithm for large r in reference
cited in Web write up.

O(|pi|) Time Substring Matching

abbb

abbbb#

abbbb#

b#

abbbb#
3

abbbabbbb#
12345678910

abbbb#

b
#

b#

6
babb

10

abbba

baba

Find All Occurrences Of pi

Search suffix tree for pi.
Suppose the search for pi is successful.
When search terminates at an element node, pi
appears exactly once in the source string S.

Search Terminates At Element Node

abbb

abbbb#

abbbb#

b#

abbbabbbb#
12345678910

abbbb#
3

abbbb#

b
#

b#
6

abbbb#

10

Search Terminates At Branch Node

When the search for pi terminates at a branch
node, each element node in the subtree rooted
at this branch node gives a different occurrence
of pi.

Search Terminates At Branch Node

abbb

abbbb#

abbbb#

b#

abbbabbbb#
12345678910

abbbb#
3

abbbb#

b
#

b#
6

ab

10

Find All Occurrences Of pi

To find all occurrences of pi in time linear in
the length of pi and linear in the number of
occurrences of pi, augment suffix tree:
Link all element nodes into a chain in inorder.
Each branch node keeps a pointer to the left most
and right most element node in its subtree.

Augmented Suffix Tree

abbb

abbbb#

abbbb#

b#

abbbabbbb#
12345678910

abbbb#
3

abbbb#

b
#

b#
6

10

Longest Repeating Substring

Find longest substring of S that occurs more
than m > 1 times in S.
Label branch nodes with number of element
nodes in subtree.
Find branch node with label >= m and max
char# field.

Longest Repeating Substring

10
abbb

abbbb#

abbbb#

b#

abbbb#
3

abbbabbbb#
12345678910

b
5
3

abbbb#

b
#

b#
6

m=2

10

m=5

Longest Common Substring

Given two strings S and T.
Find the longest common substring.
S = carport, T = airports
Longest common substring = rport
Longest common subsequence = arport

Longest common subsequence may be found in

O(|S|*|T|) time using dynamic programming.
Longest common substring may be found in
O(|S|+|T|) time using a suffix tree.

Longest Common Substring

Let $ be a new symbol.
Construct the suffix tree for the string U = S$T#.
U = carport$airports#
No repeating substring includes $.
Find longest repeating substring that is both to left and
right of $.

Find branch node that has max char# and has at

least one element node in its subtree that
represents a suffix that begins in S as well as at
least one that begins in T.