Bioinformatics : genomics and post-genomics /

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