Front matter
1-16
Multiple Genome Alignment: Chaining Algorithms Revisited
Mohamed Ibrahim Abouelhoda and Enno Ohlebusch
17-31
Two-Dimensional Pattern Matching with Rotations
Amihood Amir, Ayelet Butman, Maxime Crochemore, Gad M. Landau and Malka Schaps
32-41
An Improved Algorithm for Generalized Comparison of Minisatellites
Behshad Behzadi and Jean-Marc Steyaert
42-54
Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions
Broňa Brejová, Daniel G. Brown and Tomáš Vinař
55-69
Fast Lightweight Suffix Array Construction and Checking
Stefan Burkhardt and Juha Kärkkäinen
70-82
Distributed and Paged Suffix Trees for Large Genetic Databases
Raphaël Clifford and Marek Sergot
83-95
Analysis of Tree Edit Distance Algorithms
Serge Dulucq and Hélène Touzet
96-108
An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees
Olivier Elemento and Olivier Gascuel
109-128
Average-Optimal Multiple Approximate String Matching
Kimmo Fredriksson and Gonzalo Navarro
129-143
Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms
Raffaele Giancarlo and Marinella Sciortino
144-155
Haplotype Inference by Pure Parsimony
Dan Gusfield
156-169
A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions
Tzvika Hartman
170-185
Efficient Data Structures and a New Randomized Approach for Sorting Signed Permutations by Reversals
Haim Kaplan and Elad Verbin
186-199
Linear-Time Construction of Suffix Arrays
Extended Abstract
Dong Kyue Kim, Jeong Seop Sim, Heejin Park and Kunsoo Park
200-210
Space Efficient Linear Time Construction of Suffix Arrays
Pang Ko and Srinivas Aluru
211-224
Tuning String Matching for Huge Pattern Sets
Jari Kytöjoki, Leena Salmela and Jorma Tarhio
225-236
Sparse LCS Common Substring Alignment
Gad M. Landau, Baruch Schieber and Michal Ziv-Ukelson
237-253
On Minimizing Pattern Splitting in Multi-track String Matching
Kjell Lemström and Veli Mäkinen
254-265
Alignment between Two Multiple Alignments
Bin Ma, Zhuozhi Wang and Kaizhong Zhang
266-277
An Effective Algorithm for the Peptide
De Novo
Sequencing from MS/MS Spectrum
Bin Ma, Kaizhong Zhang and Chengzhi Liang
278-294
Pattern Discovery in RNA Secondary Structure Using Affix Trees
Giancarlo Mauri and Giulio Pavesi
295-314
More Efficient Left-to-Right Pattern Matching in Non-sequential Equational Programs
Nadia Nedjah and Luiza de Macedo Mourelle
315-327
Complexities of the Centre and Median String Problems
François Nicolas and Eric Rivals
328-347
Extracting Approximate Patterns
Extended Abstract
Johann Pelfrêne, Saïd Abdeddaïm and Joël Alexandre
348-360
A Fully Linear-Time Approximation Algorithm for Grammar-Based Compression
Hiroshi Sakamoto
361-371
Constrained Tree Inclusion
Gabriel Valiente
372-383
Working on the Problem of Sorting by Transpositions on Genome Rearrangements
Maria Emilia M. T. Walter, Luiz Reginaldo A. F. Curado and Adilton G. Oliveira
384-401
Efficient Selection of Unique and Popular Oligos for Large EST Databases
Jie Zheng, Timothy J. Close, Tao Jiang and Stefano Lonardi
Back matter