Contents
Chapter 1 Genome sequencing 1
1.1 Automatic sequencing 1
1.2 Sequencing strategies 4
1.3 Fragmentation strategies 8
1.4 Sequence assembly 12
1.5 Filling gaps 14
1.6 Obstacles to reconstruction 16
1.7 Utilizing a complementary ?large? clone library 18
1.8 The first large-scale sequencing project: The Haemophilus
influenzae genome 19
1.9 cDNA and EST 20
Chapter 2 Sequence comparisons 25
2.1 Introduction: Comparison as a sequence prediction method 25
2.2 A sample molecule: the human androsterone receptor 26
2.3 Sequence homologies ? functional homologies 27
2.4 Comparison matrices 28
2.5 The problem of insertions and deletions 33
2.6 Optimal alignment: the dynamic programming method 34
2.7 Fast heuristic methods 38
2.8 Sensitivity, specificity, and confidence level 46
2.9 Multiple alignments 50
Chapter 3 Comparative genomics 61
3.1 General properties of genomes 61
3.2 Genome comparisons 67
3.3 Gene evolution and phylogeny: applications to annotation 75
Chapter 4 Genetic information and biological sequences 85
4.1 Introduction: Coding levels 85
4.2 Genes and the genetic code 85
4.3 Expression signals 87
4.4 Specific sites 91
4.5 Sites located on DNA 91
4.6 Sites present on RNA 96
4.7 Pattern detection methods 96
Chapter 5 Statistics and sequences 107
5.1 Introduction 107
5.2 Nucleotide base and amino acid distribution 107
5.3 The biological basis of codon bias 112
5.4 Using statistical bias for prediction 113
5.5 Modeling DNA sequences 116
5.6 Complex models 120
5.7 Sequencing errors and hidden Markov models 123
5.8 Hidden Markov processes: a general sequence analysis tool 127
5.9 The search for genes ? a difficult art 127
Chapter 6 Structure prediction 131
6.1 The structure of RNA 131
6.2 Properties of the RNA molecule 132
6.3 Secondary RNA structures 134
6.4 Thermodynamic stability of RNA structures 138
6.5 Finding the most stable structure 144
6.6 Validation of predicted secondary structures 149
6.7 Using chemical and enzymatic probing to analyze folding 150
6.8 Long-distance interactions and three-dimensional structure
prediction 152
6.9 Protein structure 155
6.10 Secondary structure prediction 158
6.11 Three-dimensional modeling based on homologous protein
structure 161
6.12 Predicting folding 166
Chapter 7 Transcriptome and proteome: macromolecular networks 169
7.1 Introduction 169
7.2 Post-genomic methods 170
7.3 Macromolecular networks 182
7.4 Topology of macromolecular networks 193
7.5 Modularity and dynamics of macromolecular networks 199
7.6 Inference of regulatory networks 206
Chapter 8 Simulation of Biological Processes in the Genome Context 211
8.1 Types of simulations 213
8.2 Prediction and explanation 213
8.3 Simulation of molecular networks 215
8.4 Generic post-genomic simulators 226
Index 233