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• Half Title
• Title Page
• Copyright Page
• Preface
• A Note to the Reader
• List of Reviewers
• Contents in Brief
• Contents
• Part 1 Background Basics
• Chapter 1: The Nucleic Acid World
• Chapter 2: Protein Structure
• Chapter 3: Dealing With Databases
• Part 2 Sequence Alignments
• APPLICATIONS CHAPTER: Chapter 4: Producing and Analyzing Sequence Alignments Applications Chapter
• THEORY CHAPTER: Chapter 5: Pairwise Seq0uence Alignment and Database Searching Theory Chapter
• THEORY CHAPTER: Chapter 6: Patterns, Profiles, and Multiple Alignments Theory Chapter
• Part 3 Evolutionary Processes
• APPLICATIONS CHAPTER: Chapter 7: Recovering Evolutionary History Applications Chapter
• THEORY CHAPTER: Chapter 8: Building Phylogenetic Trees Theory Chapter
• Part 4 Genome Characteristics
• APPLICATIONS CHAPTER: Chapter 9: Revealing Genome Features Applications Chapter
• THEORY CHAPTER: Chapter 10: Gene Detection and Genome Annotation Theory Chapter
• Part 5 Secondary Structures
• APPLICATIONS CHAPTER: Chapter 11: Obtaining Secondary Structure from Sequence Applications Chapter
• THEORY CHAPTER: Chapter 12: Predicting Secondary Structures Theory Chapter
• Part 6 Tertiary Structures
• APPLICATIONS CHAPTER: Chapter 13: Modeling Protein Structure Applications Chapter
• APPLICATIONS CHAPTER: Chapter 14: Analyzing Structure–Function Relationships Applications Chapter
• Part 7 Cells and Organisms
• Chapter 15: Proteome and Gene Expression Analysis
• Chapter 16: Clustering Methods and Statistics
• Chapter 17: Systems Biology
• APPENDICES Background Theory
• Appendix A: Probability, Information, and Bayesian Analysis
• Appendix B: Molecular Energy Functions
• Appendix C: Function Optimization
• List of Symbols
• Glossary
• Index