Suffix Trees-From Genome Sequencing to Pattern Matching
Welcome
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From Genome Sequencing to Pattern Matching
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Brute Force Approach to Pattern Matching
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Herding Patterns into Trie
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Trie Construction - Pseudocode
Herding Text into Suffix Trie
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Suffix Trees
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FAQ
Slides and External References
Suffix Trees-Programming Assignment
Available Programming Languages
FAQ on Programming Assignments
Burrows-Wheeler Transform and Suffix Arrays-Burrows-Wheeler Transform
Burrows-Wheeler Transform
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Inverting Burrows-Wheeler Transform
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Using BWT for Pattern Matching
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Using BWT for Pattern Matching
Burrows-Wheeler Transform and Suffix Arrays-Suffix Arrays
Suffix Arrays
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Pattern Matching with Suffix Array
Burrows-Wheeler Transform and Suffix Arrays-Approximate Pattern Matching and Mutations of the Genome
Approximate Pattern Matching
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Burrows-Wheeler Transform and Suffix Arrays-Slides and External References
FAQ
Slides and External References
Knuth–Morris–Pratt Algorithm-Knuth-Morris-Pratt Algorithm
Exact Pattern Matching
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Skipping Positions
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Safe Shift
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Prefix Function
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Computing Prefix Function
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Implementation
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Analysis
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Knuth-Morris-Pratt Algorithm
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Programming Assignment 3 lasts for two weeks
Slides and External References
Constructing Suffix Arrays and Suffix Trees-Suffix Array Construction
Suffix Array
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General Construction Strategy
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Initialization
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Counting Sort
Sort Doubled Cyclic Shifts
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SortDouble Implementation
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Updating Classes
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UpdateClasses Implementation
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Building Suffix Array
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Slides and External References
Constructing Suffix Arrays and Suffix Trees-From Suffix Array to Suffix Tree
Suffix Array and Suffix Tree
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LCP Array
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Computing the LCP Array
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ComputeLCPArray Implementation
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Analysis
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Constructing Suffix Tree
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Implementation
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Analysis
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Slides and External References