Combinatorial Pattern Matching, 2004
15th Annual Symposium, CPM 2004, Istanbul, Turkey, July 5-7, 2004, Proceedings
Lecture Notes in Computer Science Series, Vol. 3109

This book constitutes the refereed proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching, CPM 2004, held in Istanbul, Turkey in July 2004.The 36 revised full papers presented were carefully reviewed and selected from 79 submissions. The papers are devoted to current theoretical and computational aspects of searching and matching of strings and more complicate patterns, such as trees, regular expressions, graphs, point sets, and arrays. Among the application fields addressed are computational biology, bioinformatics, genomics, proteinomics, the web, data compression, coding, multimedia, information retrieval, data analysis, pattern recognition, and computer vision.

Sorting by Reversals in Subquadratic Time.- Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs.- Sorting by Length-Weighted Reversals: Dealing with Signs and Circularity.- Optimizing Multiple Spaced Seeds for Homology Search.- Approximate Labelled Subtree Homeomorphism.- On the Average Sequence Complexity.- Approximate Point Set Pattern Matching on Sequences and Planes.- Finding Biclusters by Random Projections.- Real-Time String Matching in Sublinear Space.- On the k-Closest Substring and k-Consensus Pattern Problems.- A Trie-Based Approach for Compacting Automata.- A Simple Optimal Representation for Balanced Parentheses.- Two Algorithms for LCS Consecutive Suffix Alignment.- Efficient Algorithms for Finding Submasses in Weighted Strings.- Maximum Agreement and Compatible Supertrees.- Polynomial-Time Algorithms for the Ordered Maximum Agreement Subtree Problem.- Small Phylogeny Problem: Character Evolution Trees.- The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices.- A Computational Model for RNA Multiple Structural Alignment.- Computational Design of New and Recombinant Selenoproteins.- A Combinatorial Shape Matching Algorithm for Rigid Protein Docking.- Multi-seed Lossless Filtration.- New Results for the 2-Interval Pattern Problem.- A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes.- Sparse Normalized Local Alignment.- Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences.- Maximal Common Connected Sets of Interval Graphs.- Performing Local Similarity Searches with Variable Length Seeds.- Reversal Distance without Hurdles and Fortresses.- A Fast Set Intersection Algorithm for Sorted Sequences.- Faster Two Dimensional Pattern Matching with Rotations.- Compressed Compact Suffix Arrays.- Approximate String Matching Using Compressed Suffix Arrays.- Compressed Index for a Dynamic Collection of Texts.- Improved Single and Multiple Approximate String Matching.- Average-Case Analysis of Approximate Trie Search.