Algorithms in Bioinformatics: 4th International Workshop, WABI 2004, Bergen, Norway, September 17-21, 2004, Proceedings / Edition 1

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This book constitutes the refereed proceedings of the 4th International Workshop on Algorithms in Bioinformatics, WABI 2004, held in Bergen, Norway, in September 2004.

The 39 revised full papers presented were carefully reviewed and selected from 117 submissions. Among the topics addressed are all current issues of algorithms in bioinformatics, such as exact and approximate algorithms for genomics, genetics, sequence analysis, gene and signal recognition, alignment, molecular evolution, phylogenetics, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design.

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Table of Contents

Papers.- Reversing Gene Erosion – Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data.- Reconstructing Ancestral Gene Orders Using Conserved Intervals.- Sorting by Reversals with Common Intervals.- A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns.- A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals.- Algorithms for Finding Maximal-Scoring Segment Sets.- Gapped Local Similarity Search with Provable Guarantees.- Monotone Scoring of Patterns with Mismatches.- Suboptimal Local Alignments Across Multiple Scoring Schemes.- A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statistic.- Adding Hidden Nodes to Gene Networks.- Joint Analysis of DNA Copy Numbers and Gene Expression Levels.- Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting.- Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation.- Multiple Vector Seeds for Protein Alignment.- Solving the Protein Threading Problem by Lagrangian Relaxation.- Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations.- ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences.- Local Search Heuristic for Rigid Protein Docking.- Sequence Database Compression for Peptide Identification from Tandem Mass Spectra.- Linear Reduction for Haplotype Inference.- A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis.- Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction.- Approximation Algorithms for the Selection of Robust Tag SNPs.- The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approach.- A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences Through Alignment.- New Algorithms for Multiple DNA Sequence Alignment.- Chaining Algorithms for Alignment of Draft Sequence.- Translation Initiation Sites Prediction with Mixture Gaussian Models.- Online Consensus and Agreement of Phylogenetic Trees.- Relation of Residues in the Variable Region of 16S rDNA Sequences and Their Relevance to Genus-Specificity.- Topological Rearrangements and Local Search Method for Tandem Duplication Trees.- Phylogenetic Super-networks from Partial Trees.- Genome Identification and Classification by Short Oligo Arrays.- Novel Tree Edit Operations for RNA Secondary Structure Comparison.- The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics.- Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding.- Finding Optimal Pairs of Patterns.- Finding Missing Patterns.

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