Combinatorial Pattern Matching

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.