Combinatorial Pattern Matching

A fast bit-vector algorithm for approximate string matching based on dynamic programming.- A bit-parallel approach to suffix automata: Fast extended string matching.- A dictionary matching algorithm fast on the average for terms of varying length.- A very fast string matching algorithm for small alphabets and long patterns.- Approximate word sequence matching over Sparse Suffix Trees.- Efficient parallel algorithm for the editing distance between ordered trees.- Reporting exact and approximate regular expression matches.- An approximate oracle for distance in metric spaces.- A rotation invariant filter for two-dimensional string matching.- Constructing suffix arrays for multi-dimensional matrices.- Simple and flexible detection of contiguous repeats using a suffix tree Preliminary Version.- Comparison of coding DNA.- Fixed topology alignment with recombination.- Aligning alignments.- Efficient special cases of pattern matching with swaps.- Aligning DNA sequences to minimize the change in protein.- Genome halving.