Preface
Eugene Koonin and Michael Galperin.

Introduction: Personal Interludes

1. Genomics: From Phage to Human

1.1. The Humble Beginnings …

1.2. … and the Astonishing Progress of Genome Sequencing

1.3. Basic Questions of Comparative Genomics

1.4. Further Reading

2. Evolutionary Concept in Genetics and Genomics

2.1. Similarity, Homology, Divergence and Convergence

2.2. Patterns and Mechanisms in Genome Evolution

2.3. Conclusions and Outlook

2.4. Further Reading

3. Information Sources for Genomics

3.1. General Purpose Sequence Databases

3.2. Protein Sequence Motifs and Domain Databases

3.3. Protein Structure Databases

3.4. Specialized Genomics Databases

3.5. Organism-specific Databases

3.6. Taxonomy, Protein Interactions, and Other Databases

3.7. PubMed

3.8. Conclusions and Outlook

3.9. Further Reading

4. Principles and Methods of Sequence Analysis

4.1. Identification of Genes in a Genomic DNA Sequence

4.2. Principles of Sequence Similarity Searches

4.3. Algorithms for Sequence Alignment and Similarity Search

4.4. Practical Issues: How to Get the Most Out of BLAST

4.5. The Road to Discovery

4.6. Protein Annotation in the Absence of Detectable Homologs

4.7. Conclusions and Outlook

4.8. Further Reading

5. Genome Annotation and Analysis

5.1. Methods, Approaches and Results in Genome Annotation

5.2. Genome Context Analysis and Functional Prediction

5.3. Conclusions and Outlook

5.4. Further Reading

6. Comparative Genomics and New Evolutionary Biology

6.1. The Three Domains of Life

6.2. Prevalence of Lineage-specific Gene Loss and Horizontal Gene Transfer in Evolution

6.3. The Tree of Life: Before and After the Genomes

6.4. The Major Transitions in Evolution: A Comparative-Genomic Perspective

6.5. Conclusions and Outlook: Evolution Tinkers with Fluid Genomes

6.6. Further Reading

7. Evolution of Central Metabolic Pathways: The Playground of Non-Orthologous Gene Displacement

7.1. Carbohydrate Metabolism

7.2. Pyrimidine Biosynthesis

7.3. Purine Biosynthesis

7.4. Amino Acid Biosynthesis

7.5. Coenzyme Biosynthesis

7.6. Microbial Enzymes as Potential Drug Targets

7.7. Conclusions and Outlook

7.8. Further Reading

8. Genomes and the Protein Universe

8.1. The Protein Universe Is Highly Structured and There Are Few Common Folds

8.2. Counting the Beans: Structural Genomics, Distributions of Protein Folds and Superfamilies in Genomes and Some Models of Genome Evolution

8.3. Evolutionary Dynamics of Multidomain Proteins and Domain Accretion

8.4. Conclusions and Outlook

8.5. Further reading

9. Epilogue: Peering through the Crystal Ball

9.1. Functional Genomics: A Programme of Prediction-driven Research?

9.2. Digging Up Genomic Junkyards

9.3. “Dreams of a final theory”

Glossary

Useful Web Sites

2.1. Databases

2.2. Major Genome Sequencing Centers

Problems

Problem List

References