Combinatorial Pattern Matching

Table of Contents

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   Book Overview
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   Chapter 1 Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern
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   Chapter 2 On the Longest Common Rigid Subsequence Problem
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   Chapter 3 Text Indexing with Errors
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   Chapter 4 A New Compressed Suffix Tree Supporting Fast Search and Its Construction Algorithm Using Optimal Working Space
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   Chapter 5 Succinct Suffix Arrays Based on Run-Length Encoding
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   Chapter 6 Linear-Time Construction of Compressed Suffix Arrays Using o ( n log n )-Bit Working Space for Large Alphabets
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   Chapter 7 Faster Algorithms for δ , γ -Matching and Related Problems
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   Chapter 8 A Fast Algorithm for Approximate String Matching on Gene Sequences
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    Chapter 9 Approximate Matching in the L 1 Metric
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    Chapter 10 An Efficient Algorithm for Generating Super Condensed Neighborhoods
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    Chapter 11 The Median Problem for the Reversal Distance in Circular Bacterial Genomes
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    Chapter 12 Using PQ Trees for Comparative Genomics
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    Chapter 13 Hardness of Optimal Spaced Seed Design
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    Chapter 14 Weighted Directed Word Graph
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    Chapter 15 Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets
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    Chapter 16 An Extension of the Burrows Wheeler Transform and Applications to Sequence Comparison and Data Compression
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    Chapter 17 DNA Compression Challenge Revisited: A Dynamic Programming Approach
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    Chapter 18 On the Complexity of Sparse Exon Assembly
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    Chapter 19 An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery
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    Chapter 20 Incremental Inference of Relational Motifs with a Degenerate Alphabet
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    Chapter 21 Speeding up Parsing of Biological Context-Free Grammars
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    Chapter 22 A New Periodicity Lemma
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    Chapter 23 Two Dimensional Parameterized Matching
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    Chapter 24 An Optimal Algorithm for Online Square Detection
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    Chapter 25 A Simple Fast Hybrid Pattern-Matching Algorithm
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    Chapter 26 Prefix-Free Regular-Expression Matching
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    Chapter 27 Reducing the Size of NFAs by Using Equivalences and Preorders
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    Chapter 28 Regular Expression Constrained Sequence Alignment
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    Chapter 29 A Linear Tree Edit Distance Algorithm for Similar Ordered Trees
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    Chapter 30 A Polynomial Time Matching Algorithm of Ordered Tree Patterns Having Height-Constrained Variables
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    Chapter 31 Assessing the Significance of Sets of Words
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    Chapter 32 Inferring a Graph from Path Frequency
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    Chapter 33 Exact and Approximation Algorithms for DNA Tag Set Design
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    Chapter 34 Parametric Analysis for Ungapped Markov Models of Evolution
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    Chapter 35 Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements
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    Chapter 36 Identifying Similar Surface Patches on Proteins Using a Spin-Image Surface Representation
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    Chapter 37 Mass Spectra Alignments and Their Significance