Algorithms in Bioinformatics

Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003. Proceedings

Editors:

ISBN: 978-3-540-20076-5 (Print) 978-3-540-39763-2 (Online)

Table of contents (36 chapters)

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  1. Front Matter

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  2. Comparative Genomics

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      Pages 1-16

      A Local Chaining Algorithm and Its Applications in Comparative Genomics

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      Pages 17-24

      Common Intervals of Two Sequences

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      Pages 25-38

      A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring

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      Pages 39-54

      Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity

  3. Gene Finding and Expression

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      Pages 55-62

      A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods

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      Pages 63-77

      A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence

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      Pages 78-94

      Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency

  4. Genome Mapping

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      Pages 95-110

      New Algorithm for the Simplified Partial Digest Problem

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      Pages 111-123

      Noisy Data Make the Partial Digest Problem NP-hard

  5. Pattern and Motif Discovery

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      Pages 124-138

      Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions

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      Pages 139-150

      A Combinatorial Approach to Automatic Discovery of Cluster-Patterns

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      Pages 151-164

      Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology

  6. Phylogenetic Analysis

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      Pages 165-176

      Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees

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      Pages 177-189

      Efficient Generation of Uniform Samples from Phylogenetic Trees

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      Pages 190-201

      New Efficient Algorithm for Detection of Horizontal Gene Transfer Events

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      Pages 202-215

      Ancestral Maximum Likelihood of Evolutionary Trees Is Hard

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      Pages 216-227

      A Linear-Time Majority Tree Algorithm

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      Pages 228-244

      Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model

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      Pages 245-258

      Better Hill-Climbing Searches for Parsimony

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      Pages 259-270

      Computing Refined Buneman Trees in Cubic Time

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