The 16th Annual Symposium on Combinatorial Pattern Matching was held on Jeju Island, Korea on June 19 22, 2005. Previous meetings were held in Paris, London, Tucson, Padova, Asilomar, Helsinki, Laguna Beach, Aarhus, Piscataway,Warwick,Montreal,Jerusalem,Fukuoka, Morelia,and Istanbul over the years 1990 2004. In response to the call for papers, CPM 2005 received a record number of 129papers.Eachsubmissionwasreviewedbyatleast threeProgramCommittee members with the assistance of external referees. Since there were many hi- quality papers, the Program Committee s task was extremely di?cult. Through an extensive discussion the Program Committee accepted 37 of the submissions tobepresentedattheconference.Theyconstituteoriginalresearchcontributions in combinatorial pattern matching and its applications. Inadditiontotheselectedpapers,CPM2005hadthreeinvitedpresentations, by Esko Ukkonen from the University of Helsinki, Ming Li from the University of Waterloo, and Naftali Tishby from The Hebrew University of Jerusalem. We would like to thank all Program Committee members and external r- erees for their excellent work, especially given the demanding time constraints; they gave the conference its distinctive character. We also thank all who s- mitted papers for consideration; they all contributed to the high quality of the conference. Finally, we thank the Organizing Committee members and the graduates- dents who worked hard to put in place the logistical arrangements of the c- ference. It is their dedicated contribution that made the conference possible and enjoyable.

Includes supplementary material: sn.pub/extras

Inhalt
Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern.- On the Longest Common Rigid Subsequence Problem.- Text Indexing with Errors.- A New Compressed Suffix Tree Supporting Fast Search and Its Construction Algorithm Using Optimal Working Space.- Succinct Suffix Arrays Based on Run-Length Encoding.- Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets.- Faster Algorithms for ?,?-Matching and Related Problems.- A Fast Algorithm for Approximate String Matching on Gene Sequences.- Approximate Matching in the L 1 Metric.- An Efficient Algorithm for Generating Super Condensed Neighborhoods.- The Median Problem for the Reversal Distance in Circular Bacterial Genomes.- Using PQ Trees for Comparative Genomics.- Hardness of Optimal Spaced Seed Design.- Weighted Directed Word Graph.- Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets.- An Extension of the Burrows Wheeler Transform and Applications to Sequence Comparison and Data Compression.- DNA Compression Challenge Revisited: A Dynamic Programming Approach.- On the Complexity of Sparse Exon Assembly.- An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery.- Incremental Inference of Relational Motifs with a Degenerate Alphabet.- Speeding up Parsing of Biological Context-Free Grammars.- A New Periodicity Lemma.- Two Dimensional Parameterized Matching.- An Optimal Algorithm for Online Square Detection.- A Simple Fast Hybrid Pattern-Matching Algorithm.- Prefix-Free Regular-Expression Matching.- Reducing the Size of NFAs by Using Equivalences and Preorders.- Regular Expression Constrained Sequence Alignment.- A Linear Tree Edit Distance Algorithm for Similar Ordered Trees.- A Polynomial Time Matching Algorithmof Ordered Tree Patterns Having Height-Constrained Variables.- Assessing the Significance of Sets of Words.- Inferring a Graph from Path Frequency.- Exact and Approximation Algorithms for DNA Tag Set Design.- Parametric Analysis for Ungapped Markov Models of Evolution.- Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements.- Identifying Similar Surface Patches on Proteins Using a Spin-Image Surface Representation.- Mass Spectra Alignments and Their Significance.