Suffix Trees

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Suffix Trees

• ALGGEN Algorithmics and genetics group
• Dep. Llenguatges i Sistemes Informàtics
• Universitat Politècnica de Catalunya

Dr. Xavier Messeguer
http//www.lsi.upc.es/alggen
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Suffix trees
Given string ababaas
Suffixes
3 abaas
1 ababaas
4 baas
2 babaas
What kind of queries?
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Queries on Suffix trees

• 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
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Quadratic Insertion algorithm
Given the string ababaabbs
ababaabbs,1
babaabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
ababaabbs,1
babaabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
babaabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
babaabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
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Quadratic Insertion algorithm
Given the string ababaabbs
ba
baabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
ba
baabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
ba
baabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
ba
ba
baabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
ba
baabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
ba
baabbs,2
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Quadratic Insertion algorithm
Given the string ababaabbs
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Quadratic Insertion algorithm
Given the string ababaabbs
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Quadratic Insertion algorithm
Given the string ababaabbs
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Quadratic Insertion algorithm
Given the string ababaabbs
ba
baabbs,2
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Definition of MUM
Matching
Unique
Maximal
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Search for MUMs
Given strings ababaabs and aabaat
1st Bottom-up traversal
(Through the tree)
List of UM aab,abaa,baa.
2nd Search for maximals
(through the list of UM)
MUMs aab,abaa.