Combinatorial Pattern Matching

Table of Contents

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   Book Overview
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   Chapter 1 Asynchronous Pattern Matching
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   Chapter 2 SNP and Haplotype Analysis – Algorithms and Applications
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   Chapter 3 Identifying Co-referential Names Across Large Corpora
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   Chapter 4 Adaptive Searching in Succinctly Encoded Binary Relations and Tree-Structured Documents
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   Chapter 5 Theoretical and Practical Improvements on the RMQ-Problem, with Applications to LCA and LCE
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   Chapter 6 A Linear Size Index for Approximate Pattern Matching
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   Chapter 7 On-Line Linear-Time Construction of Word Suffix Trees
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   Chapter 8 Obtaining Provably Good Performance from Suffix Trees in Secondary Storage
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    Chapter 9 Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures
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    Chapter 10 New Bounds for Motif Finding in Strong Instances
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    Chapter 11 Fingerprint Clustering with Bounded Number of Missing Values
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    Chapter 12 Tiling an Interval of the Discrete Line
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    Chapter 13 Common Substrings in Random Strings
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    Chapter 14 On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem
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    Chapter 15 Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms
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    Chapter 16 Solving the Maximum Agreement SubTree and the Maximum Compatible Tree Problems on Many Bounded Degree Trees
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    Chapter 17 An Improved Algorithm for the Macro-evolutionary Phylogeny Problem
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    Chapter 18 Property Matching and Weighted Matching
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    Chapter 19 Faster Two Dimensional Scaled Matching
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    Chapter 20 Approximation of RNA Multiple Structural Alignment
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    Chapter 21 Finding Common RNA Pseudoknot Structures in Polynomial Time
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    Chapter 22 A Compact Mathematical Programming Formulation for DNA Motif Finding
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    Chapter 23 Local Alignment of RNA Sequences with Arbitrary Scoring Schemes
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    Chapter 24 An $O(n^{3/2}\sqrt{\log (n)})$ Algorithm for Sorting by Reciprocal Translocations
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    Chapter 25 Longest Common Subsequences in Permutations and Maximum Cliques in Circle Graphs
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    Chapter 26 A Simpler Analysis of Burrows-Wheeler Based Compression
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    Chapter 27 Statistical Encoding of Succinct Data Structures
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    Chapter 28 Dynamic Entropy-Compressed Sequences and Full-Text Indexes
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    Chapter 29 Reducing the Space Requirement of LZ-Index
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    Chapter 30 Faster Algorithms for Computing Longest Common Increasing Subsequences
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    Chapter 31 New Algorithms for Text Fingerprinting
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    Chapter 32 Sublinear Algorithms for Parameterized Matching
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    Chapter 33 Approximate Matching in Weighted Sequences
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    Chapter 34 Algorithms for Finding a Most Similar Subforest
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    Chapter 35 Efficient Algorithms for Regular Expression Constrained Sequence Alignment
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    Chapter 36 Large Scale Matching for Position Weight Matrices