Bioinformatics (eBook)

Genomics and Post-Genomics

Fr d ric Dardel, Fran ois K p s (Autoren)

eBook Download: PDF

2007
Wiley (Verlag)
978-0-470-02002-9 (ISBN)

Infos

This book is an excellent introductory text describing the use of bioinformatics to analyze genomic and post-genomic data. It has been translated from the original popular French edition, which was based on a course taught at the well-respected cole Polytechnique in Palaiseau. This edition has been fully revised and updated by the authors. After a brief introduction to gene structure and sequence determination, it describes the techniques used to identify genes, their protein-coding sequences and regulatory regions. The book discusses the methodology of comparative genomics, using information from different organisms to deduce information about unknown sequences. There is a comprehensive chapter on structure prediction, covering both RNA and protein. Finally, the book describes the complex networks of RNA and protein that exist within the cell and their interactions, ending with a discussion of the simulation approaches that can be used to model these networks. Praise from the reviews: In context of the new developments the genomic era has brought, Bioinformatics: Genomics and Post-Genomics becomes a fundamental and indispensable resource for undergraduate and early graduate students insightfully authored will immensely help students in establishing important foundations while shaping their careers. NEWSLETTER, BRITISH SOCIETY OF CELL BIOLOGY

Autor

Frédéric Dardel. LCRB - UMR8015 CNRS, Faculté de Pharmacie, Université René Descartes/Paris. François Képès. Epigenomics Project, Genopole®, Bldg G3, 93 rue Henri Rochefort, 91000 Evry, France. Translated by Noah Hardy.

Inhalt

Chapter 1. Genome sequencing.

1.1 Automatic sequencing.

1.2 Sequencing strategies.

1.3 Fragmentation strategies.

1.4 Sequence assembly.

1.5 Filling gaps.

1.6 Obstacles to reconstruction.

1.7 Utilizing a complementary 'large' clone
library.

1.8 The first large-scale sequencing project: The Haemophilus
influenzae genome.

1.9 cDNA and EST.

Chapter 2. Sequence comparisons.

2.1 Introduction: Comparison as a sequence prediction
method.

2.2 A sample molecule: the human and rosterone receptor.

2.3 Sequence homologies - functional homologies.

2.4 Comparison matrices.

2.5 The problem of insertions and deletions.

2.6 Optimal alignment: the dynamic programming method.

2.7 Fast heuristic methods.

2.8 Sensitivity, specificity, and confidence level.

2.9 Multiple alignments.

Chapter 3. Comparative genomics.

3.1 General properties of genomes.

3.2 Genome comparisons.

3.3 Gene evolution and phylogeny: applications to
annotation.

Chapter 4. Genetic information and biological sequences.

4.1 Introduction: Coding levels.

4.2 Genes and the genetic code.

4.3 Expression signals.

4.4 Specific sites.

4.5 Sites located on DNA.

4.6 Sites present on RNA.

4.7 Pattern detection methods.

Chapter 5. Statistics and sequences.

5.1 Introduction.

5.2 Nucleotide base and amino acid distribution.

5.3 The biological basis of codon bias.

5.4 Using statistical bias for prediction.

5.5 Modeling DNA sequences.

5.6 Complex models.

5.7 Sequencing errors and hidden Markov models.

5.8 Hidden Markov processes: a general sequence analysis
tool.

5.9 The search for genes - a difficult art.

Chapter 6. Structure prediction.

6.1 The structure of RNA.

6.2 Properties of the RNA molecule.

6.3 Secondary RNA structures.

6.4 Thermodynamic stability of RNA structures.

6.5 Finding the most stable structure.

6.6 Validation of predicted secondary structures.

6.7 Using chemical and enzymatic probing to analyze folding.

6.8 Long-distance interactions and three-dimensional structure
prediction.

6.9 Protein structure.

6.10 Secondary structure prediction.

6.11 Three-dimensional modeling based on homologous protein
structure.

6.12 Predicting folding.

Chapter 7. Transcriptome and proteome: macromolecular
networks.

7.1 Introduction.

7.2 Post-genomic methods.

7.3 Macromolecular networks.

7.4 Topology of macromolecular networks.

7.5 Modularity and dynamics of macromolecular networks.

7.6 Inference of regulatory networks.

Chapter 8. Simulation of Biological Processes in the Genome
Context.

8.1 Types of simulations.

8.2 Prediction and explanation.

8.3 Simulation of molecular networks.

8.4 Generic post-genomic simulators.

Index.

Rezensionen

"...provides a clear and concise introduction to the popular new science of bioinformatics." (Bioautomation, volume 7)

Produkt-Details

• Erscheint lt. Verlag: 11.1.2007
• Übersetzer: Noah Hardy
• Sprache: englisch
• Themenwelt: Mathematik / Informatik ► Informatik ► Theorie / Studium
• Themenwelt: Informatik ► Weitere Themen ► Bioinformatik
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Chemie
• Themenwelt: Technik
• Schlagworte: Automatic • Bioinformatics & Computational Biology • Bioinformatik • Bioinformatik u. Computersimulationen in der Biowissenschaften • Biowissenschaften • Complementary • dynamic • First • Genetics • Genetik • Genome • genomics • haemophilus • homologies • influenzae • Insertions • introduction comparison • largescale • Library • Life Sciences • Method • obstacles • Prediction Method • Problem • programming • receptor • Sample • Sequence • sequencing
• ISBN-10: 0-470-02002-4 / 0470020024
• ISBN-13: 978-0-470-02002-9 / 9780470020029