Algorithms in Bioinformatics

Table of Contents

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   Book Overview
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   Chapter 1 A Local Chaining Algorithm and Its Applications in Comparative Genomics
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   Chapter 2 Common Intervals of Two Sequences
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   Chapter 3 A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring
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   Chapter 4 Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity
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   Chapter 5 A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods
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   Chapter 6 A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence
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   Chapter 7 Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency
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   Chapter 8 New Algorithm for the Simplified Partial Digest Problem
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    Chapter 9 Noisy Data Make the Partial Digest Problem NP -hard
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    Chapter 10 Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions
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    Chapter 11 A Combinatorial Approach to Automatic Discovery of Cluster-Patterns
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    Chapter 12 Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology
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    Chapter 13 Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees
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    Chapter 14 Efficient Generation of Uniform Samples from Phylogenetic Trees
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    Chapter 15 New Efficient Algorithm for Detection of Horizontal Gene Transfer Events
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    Chapter 16 Ancestral Maximum Likelihood of Evolutionary Trees Is Hard
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    Chapter 17 A Linear-Time Majority Tree Algorithm
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    Chapter 18 Algorithms in Bioinformatics
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    Chapter 19 Better Hill-Climbing Searches for Parsimony
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    Chapter 20 Computing Refined Buneman Trees in Cubic Time
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    Chapter 21 Distance Corrections on Recombinant Sequences
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    Chapter 22 Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks
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    Chapter 23 Identifying Blocks and Sub-populations in Noisy SNP Data
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    Chapter 24 Designing Optimally Multiplexed SNP Genotyping Assays
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    Chapter 25 Minimum Recombinant Haplotype Configuration on Tree Pedigrees
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    Chapter 26 Efficient Energy Computation for Monte Carlo Simulation of Proteins
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    Chapter 27 Speedup LP Approach to Protein Threading via Graph Reduction
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    Chapter 28 Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment
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    Chapter 29 Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power
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    Chapter 30 A Large Version of the Small Parsimony Problem
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    Chapter 31 Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree
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    Chapter 32 Composition Alignment
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    Chapter 33 Match Chaining Algorithms for cDNA Mapping
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    Chapter 34 Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt
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    Chapter 35 Bounds for Resequencing by Hybridization
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    Chapter 36 Selecting Degenerate Multiplex PCR Primers