Combinatorial Pattern Matching

The refereed proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching, CPM 2003, held in Morelia, Michoacán, Mexico in June 2003.

The 28 revised full papers presented were carefully reviewed and selected from 57 submissions. The papers are devoted to current theoretical and computational aspects of searching and matching strings and more complicated patterns, such as trees, regular expressions, graphs, point sets, and arrays. Among the application fields addressed are computational biology, bioinformatics, genomics, the Web, data compression, coding, multimedia, information retrieval, pattern recognition, and computer vision.

Inhalt

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.