Combinatorial Pattern Matching

Multiple Genome Alignment: Chaining Algorithms Revisited.- Two-Dimensional Pattern Matching with Rotations.- An Improved Algorithm for Generalized Comparison of Minisatellites.- Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions.- Fast Lightweight Suffix Array Construction and Checking.- Distributed and Paged Suffix Trees for Large Genetic Databases.- Analysis of Tree Edit Distance Algorithms.- An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees.- Average-Optimal Multiple Approximate String Matching.- Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms.- Haplotype Inference by Pure Parsimony.- A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions.- Efficient Data Structures and a New Randomized Approach for Sorting Signed Permutations by Reversals.- Linear-Time Construction of Suffix Arrays.- Space Efficient Linear Time Construction of Suffix Arrays.- Tuning String Matching for Huge Pattern Sets.- Sparse LCS Common Substring Alignment.- On Minimizing Pattern Splitting in Multi-track String Matching.- Alignment between Two Multiple Alignments.- An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum.- Pattern Discovery in RNA Secondary Structure Using Affix Trees.- More Efficient Left-to-Right Pattern Matching in Non-sequential Equational Programs.- Complexities of the Centre and Median String Problems.- Extracting Approximate Patterns.- A Fully Linear-Time Approximation Algorithm for Grammar-Based Compression.- Constrained Tree Inclusion.- Working on the Problem of Sorting by Transpositions on Genome Rearrangements.- Efficient Selection of Unique and Popular Oligos for Large EST Databases.