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| Genome sequencing | |
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| Automatic sequencing | |
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| Sequencing strategies | |
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| Fragmentation strategies | |
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| Sequence assembly | |
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| Filling gaps | |
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| Obstacles to reconstruction | |
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| Utilizing a complementary 'large' clone library | |
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| The first large-scale sequencing project: The Haemophilus influenzae genome | |
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| cDNA and EST | |
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| Sequence comparisons | |
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| Introduction: Comparison as a sequence prediction method | |
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| A sample molecule: the human and rosterone receptor | |
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| Sequence homologies - functional homologies | |
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| Comparison matrices | |
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| The problem of insertions and deletions | |
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| Optimal alignment: the dynamic programming method | |
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| Fast heuristic methods | |
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| Sensitivity, specificity, and confidence level | |
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| Multiple alignments | |
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| Comparative genomics | |
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| General properties of genomes | |
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| Genome comparisons | |
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| Gene evolution and phylogeny: applications to annotation | |
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| Genetic information and biological sequences | |
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| Introduction: Coding levels | |
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| Genes and the genetic code | |
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| Expression signals | |
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| Specific sites | |
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| Sites located on DNA | |
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| Sites present on RNA | |
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| Pattern detection methods | |
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| Statistics and sequences | |
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| Introduction | |
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| Nucleotide base and amino acid distribution | |
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| The biological basis of codon bias | |
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| Using statistical bias for prediction | |
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| Modeling DNA sequences | |
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| Complex models | |
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| Sequencing errors and hidden Markov models | |
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| Hidden Markov processes: a general sequence analysis tool | |
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| The search for genes - a difficult art | |
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| Structure prediction | |
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| The structure of RNA | |
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| Properties of the RNA molecule | |
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| Secondary RNA structures | |
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| Thermodynamic stability of RNA structures | |
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| Finding the most stable structure | |
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| Validation of predicted secondary structures | |
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| Using chemical and enzymatic probing to analyze folding | |
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| Long-distance interactions and three-dimensional structure prediction | |
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| Protein structure | |
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| Secondary structure prediction | |
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| Three-dimensional modeling based on homologous protein structure | |
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| Predicting folding | |
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| Transcriptome and proteome: macromolecular networks | |
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| Introduction | |
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| Post-genomic methods | |
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| Macromolecular networks | |
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| Topology of macromolecular networks | |
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| Modularity and dynamics of macromolecular networks | |
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| Inference of regulatory networks | |
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| Simulation of Biological Processes in the Genome Context | |
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| Types of simulations | |
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| Prediction and explanation | |
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| Simulation of molecular networks | |
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| Generic post-genomic simulators | |
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| Index | |