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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 | |