Combinatorial Pattern Matching

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

Includes supplementary material: sn.pub/extras