Algorithms in Bioinformatics: First International Workshop, WABI 2001 Århus Denmark, August 28–31, 2001 Proceedings

Description

This book constitutes the refereed proceedings of the First International Workshop on Algorithms in Bioinformatics, WABI 2001, held in Aarhus, Denmark, in August 2001. The 23 revised full papers presented were carefully reviewed and selected from more than 50 submissions. Among the issues addressed are exact and approximate algorithms for genomics, sequence analysis, gene and signal recognition, alignment, molecular evolution, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design; methodological topics from algorithmics; high-performance approaches to hard computational problems in bioinformatics. An Improved Model for Statistical Alignment....Pages 1-10 Improving Profile-Profile Alignments via Log Average Scoring....Pages 11-26 False Positives in Genomic Map Assembly and Sequence Validation....Pages 27-40 Boosting EM for Radiation Hybrid and Genetic Mapping....Pages 41-51 Placing Probes along the Genome Using Pairwise Distance Data....Pages 52-68 Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar....Pages 69-84 Assessing the Statistical Significance of Overrepresented Oligonucleotides....Pages 85-97 Pattern Matching and Pattern Discovery Algorithms for Protein Topologies....Pages 98-111 Computing Linking Numbers of a Filtration....Pages 112-127 Side Chain-Positioning as an Integer Programming Problem....Pages 128-141 A Chemical-Distance-Based Test for Positive Darwinian Selection....Pages 142-155 Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time....Pages 156-163 Experiments in Computing Sequences of Reversals....Pages 164-174 Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes....Pages 175-188 Finding an Optimal Inversion Median: Experimental Results....Pages 189-203 Analytic Solutions for Three-Taxon ML MC Trees with Variable Rates Across Sites....Pages 204-213 The Performance of Phylogenetic Methods on Trees of Bounded Diameter....Pages 214-226 (1+ε)-Approximation of Sorting by Reversals and Transpositions....Pages 227-237 On the Practical Solution of the Reversal Median Problem....Pages 238-251 Algorithms for Finding Gene Clusters....Pages 252-263 Determination of Binding Amino Acids Based on Random Peptide Array Screening Data....Pages 264-277 A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites....Pages 278-293 Comparing Assemblies Using Fragments and Mate-Pairs....Pages 294-306