suffix trees alggen: algorithmics and genetics group dep. llenguatges i sistemes informàtics...
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Suffix Trees
ALGGEN: Algorithmics and genetics group
Dep. Llenguatges i Sistemes Informàtics
Universitat Politècnica de Catalunya
Dr. Xavier Messeguerhttp://www.lsi.upc.es/~alggen
Suffix trees
Given string ababaas:
1: ababaas
2: babaas
3: abaas
4: baas
5: aas
6: as
7: s
as,3
s,6
as,5
s,7
as,4ba
baas,2
a
babaas,1
a
babaas,1
ba
baas,2
as,3
as,4
s,6
as,5
s,7
Suffixes:
What kind of queries?
Queries on Suffix trees
a
babaas,1as,3
ba
baas,2
as,4
s,6
as,5
s,7
• Does the sequence ababaas contain any ocurrence of patterns abab, aab, and ab?
• Find repeats within the sequence ababaas.
…………………………
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Quadratic Insertion algorithm
Given the string ababaabbs
ababaabbs,1
abbs,3
abbs,4ba
baabbs,2
abbs,4
abbs,3ba
a
baabbs,1
Quadratic Insertion algorithm
Given the string ababaabbs
abbs,4ba
baabbs,2
abbs,4
abbs,3ba
a
baabbs,1
abbs,5
Quadratic Insertion algorithm
Given the string ababaabbs
abbs,4ba
baabbs,2
abbs,4
abbs,3ba
a
baabbs,1
abbs,5
Quadratic Insertion algorithm
Given the string ababaabbs
abbs,4
ba
ba
baabbs,2
abbs,4
a abbs,5
b
a abbs,3
baabbs,1
Quadratic Insertion algorithm
Given the string ababaabbs
abbs,4ba
baabbs,2
abbs,4
a abbs,5
b
a abbs,3
baabbs,1
bs,6
Quadratic Insertion algorithm
Given the string ababaabbs
abbs,4ba
baabbs,2
abbs,4
a abbs,5
b
a abbs,3
baabbs,1
bs,6
Quadratic Insertion algorithm
Given the string ababaabbs
a abbs,5
b
a abbs,3
baabbs,1
bs,6
a
baabbs,2
b
abbs,4
bs,7
Quadratic Insertion algorithm
Given the string ababaabbs
a abbs,5
b
a abbs,3
baabbs,1
bs,6
a
baabbs,2
b
abbs,4
bs,7
s,7
Quadratic Insertion algorithm
Given the string ababaabbs
a abbs,5
b
a abbs,3
baabbs,1
bs,6
a
baabbs,2
b
abbs,4
bs,7
s,7
s,7
Quadratic Insertion algorithm
Given the string ababaabbs
abbs,4ba
baabbs,2
abbs,4
a abbs,5
b
a abbs,3
baabbs,1
bs,6
a
baabbs,2
b
abbs,4