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| Molecular Biology and Biological Chemistry | |
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| The Genetic Material | |
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| Gene Structure and Information Content | |
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| Protein Structure and Function | |
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| The Nature of Chemical Bonds | |
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| Molecular Biology Tools | |
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| Genomic Information Content | |
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| Data Searches and Pairwise Alignments | |
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| Dot Plots | |
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| Simple Alignments | |
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| Gaps | |
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| Scoring Matrices | |
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| Dynamic Programming: The Needleman and Wunsch Algorithm | |
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| Global and Local Alignments | |
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| Database Searches | |
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| Multiple Sequence Alignments | |
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| Substitution Patterns | |
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| Patterns of Substitutions within Genes | |
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| Estimating Substitution Numbers | |
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| Variations in Evolutionary Rates between Genes | |
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| Molecular Clocks | |
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| Evolution in Organelles | |
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| Distance-Based Methods of Phylogenetics | |
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| History of Molecular Phylogenetics | |
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| Advantages to Molecular Phylogenies | |
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| Phylogenetic Trees | |
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| Distance Matrix Methods | |
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| Maximum Likelihood Approaches | |
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| Multiple Sequence Alignments | |
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| Character-Based Methods of Phylogenetics | |
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| Parsimony | |
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| Inferred Ancestral Sequences | |
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| Strategies for Faster Searches | |
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| Consensus Trees | |
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| Tree Confidence | |
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| Comparison of Phylogenetic Methods | |
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| Molecular Phylogenies | |
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| Genomics and Gene Recognition | |
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| Prokaryotic Genomes | |
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| Prokaryotic Gene Structure | |
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| GC Content in Prokaryotic Genomes | |
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| Prokaryotic Gene Density | |
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| Eukaryotic Genomes | |
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| Eukaryotic Gene Structure | |
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| Open Reading Frames | |
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| GC Content in Eukaryotic Genomes | |
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| Gene Expression | |
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| Transposition | |
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| Repetitive Elements | |
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| Eukaryotic Gene Density | |
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| Protein and RNA Structure Prediction | |
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| Amino Acids | |
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| Polypeptide Composition | |
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| Secondary Structure | |
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| Tertiary and Quaternary Structure | |
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| Algorithms for Modeling Protein Folding | |
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| Structure Prediction | |
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| Predicting RNA Secondary Structures | |
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| Proteomics | |
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| From Genomes to Proteomes | |
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| Protein Classification | |
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| Experimental Techniques | |
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| Inhibitors and Drug Design | |
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| Ligand Screening | |
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| X-Ray Crystal Structures | |
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| NMR Structures | |
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| Empirical Methods and Prediction Techniques | |
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| Post-Translational Modification Prediction | |
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| A Gentle Introduction to Computer Programming and Data Structures | |
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| Enzyme Kinetics | |
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| Sample Programs in Perl | |
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| Glossary | |
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| Solutions to Selected Problems | |
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| Index | |