Bioinformatics provides a clear and concise introduction to the use of bioinformatics to analyze genomic data.

Features:

• Covers basic studies of the genome as well as more advanced post-genomic analysis
• Features both biological problems and concepts from informatics
• Translated from a successful French edition that was itself based on a course at the well-respected Ecole Polytechnique in Paris

Contents

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

• 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

• 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

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