Ch. 1. The Nucleic Acid World -- Ch. 2. Protein Structure -- Ch. 3. Dealing with Databases -- Ch. 4. Producing and Analyzing Sequence Alignments -- Ch. 5. Pairwise Sequence Alignment and Database Searching -- Ch. 6. Patterns, Profiles, and Multiple Alignments -- Ch. 7. Recovering Evolutionary History -- Ch. 8. Building Phylogenetic Trees -- Ch. 9. Revealing Genome Features -- Ch. 10. Gene Detection and Genome Annotation -- Ch. 11. Obtaining Secondary Structure from Sequence -- Ch. 12. Predicting Secondary Structures -- Ch. 13. Modeling Protein Structure -- Ch. 14. Analyzing Structure-Function Relationships -- Ch. 15. Proteome and Gene Expression Analysis -- Ch. 16. Clustering Methods and Statistics -- Ch. 17. Systems Biology -- App. A. Probability, Information, and Bayesian Analysis -- App. B. Molecular Energy Functions -- App. C. Function Optimization.