생명 정보학 입문서. 이 책은 생명정보학의 전반적인 상황을 담아 정리한 것으로 기초부터 단백질체학에 이르기는 내용으로 구성했다.

Contents 1. Molecular Biology and Biological Chemistry 1 The Genetic Material 2 Nucleotides 2 Orientation 3 Base pairing 5 The central dogma of molecular biology 7 Gene Structure and Information Content 8 Promoter sequences 8 The genetic code 9 Open reading frames 10 Introns and exons 13 Protein Structure and Function 14 Primary structure 14 Secondary, tertiary, and quaternary structure 16 The Nature of Chemical Bonds 16 Anatomy of an atom 17 Valence 19 Electronegativity 20 Hydrophilicity and hydrophobicity 21 Chapter Summary 22 Readings for Greater Depth 22 Questions and Problems 23 2. Data Searches and Pairwise Alignments 25 Dot Plots 26 Simple Alignments 28 Gaps 29 Simple gap penalties 29 Origination and length penalties 30 Scoring Matrices 31 Dynamic Programming: The Needleman and Wunsch Algorithm 35 Global and Local Alignments 39 Semiglobal alignments 39 The smith-waterman algorithm 41 Database Searches 43 BLAST and Its relatives 43 FASTA and related algorithm n 45 Alignment scores and statistical significance of database searches 47 Multiple Sequence Alignments 48 Chapter Summary 49 Readings for Greater Depth 50 Questions and Problems 51 3. Substitution Patterns 53 Patterns of Substitutions within Genes 54 Mutation rates 54 Functional constraint 55 Synonymous vs. nonsynonymous substitutions 57 Indels and pseudogenes 58 Substitutions vs. mutations 59 Fixation 60 Estimating Substitution Numbers 62 Jukes-cantor model 63 Transitions and transversions 64 Kimura's two-parameter model 64 Models with even more parameters 66 Substitutions between protein sequences 67 Variations in Evolutionary Rates between Genes 68 Molecular Clocks 69 Relative rate test 70 Causes of rate variation in lineages 72 Evolution in Organelles 72 Chapter Summary 73 Readings for Greater Depth 74 Questions and Problems 74 4. Distance-Based Methods of Phylogenetics 77 History of Molecular Phylogenetics 78 Advantages to Molecular Phylogenies 79 Phylogenetic Trees 81 Terminology of tree reconstruction 81 Rooted and unrooted trees 82 Gene vs. species trees 84 Character and distance data 85 Distance Matrix Methods 87 UPGMA 87 Estimation of branch lengths 90 Transformed distance method 91 Neighbor's relation method 93 Neighbor-joining methods 94 Maximum Likelihood Approaches 95 Multiple Sequence Alignments 95 Chapter Summary 96 Readings for Greater Depth 97 Questions and Problems 97 5. Character-Based Methods of Phylogenetics 99 Parsimony 100 Informative and uninformative sites 100 Unweighted parsimony 102 Weighted parsimony 106 Inferred Ancestral Sequences 107 Strategies for Faster Searches 108 Branch and bound 108 Heuristic searches 110 Consensus Trees 112 Tree Confidence 112 Bootstrapping 113 Parametric tests 115 Comparison of Phylogenetic Methods 116 Molecular Phylogenies 116 The tree of life 116 Human origins 118 Chapter Summary 119 Readings for Greater Depth 119 Questions and Problems 120 6. Genomics and Gene Recognition 121 Prokaryotic Genomes 122 Prokaryotic Gene Structure 124 Promoter elements 125 Open Reading frames 128 Conceptual translation 129 Termination sequences 129 GC Contents in Prokaryotic Genome 130 Prokaryotic Gene Density 131 Eukaryotic Genomes 131 Eukaryotic Gene Structure 132 Promoter elements 133 Regulatory protein binding sites 136 Open Reading Frames 137 Introns and exons 138 Alternative splicing 139 GC Content in Eukaryotic Genomes 141 CpG islands 143 Isochores 145 Codon usage bias 147 Gene Expression 147 cDNAs and ESTs 147 Serial analysis of gene expression 149 Microarrays 150 Transposition 152 Repetitive Elements 153 Eukaryotic Gene Density 155 Chapter Summary 155 Readings for Greater Depth 156 Questions and Problems 157 7. Protein and RNA Structure Prediction 159 Amino Acids 160 Polypeptide Composition 164 Secondary Structure 164 Backbone flexibility, φ and ψ 164 Accuracy of predictions 166 The chou-fasman and GOR methods 167 Tertiary and Quaternary Structure 169 Hydrophobicity 171 Disulfide bonds 171 Active structures vs. most stable structures 172 Algorithms for Modeling Protein Folding 173 Lattice models 173 Off-lattice models 176 Energy functions and optimization 176 Structure Prediction 178 Comparative modeling 179 Threading: reverse protein folding 180 Predicting RNA Secondary Structures 181 Chapter Summary 183 Readings for Greater Depth 184 Questions and Problems 185 8. Proteomics 187 From Genomes to Proteomes 188 Protein Classification 188 Enzyme nomenclature 189 Families and superfamilies 190 Folds 191 Experimental Techniques 192 2D electrophoresis 192 Mass spectrometry 194 Protein microarrays 195 Inhibitors and Drug Design 196 Ligand Screening 197 Ligand docking 197 Database screening 199 X-Ray Crystal Structures 200 NMR Structures 205 Empirical Methods and Prediction Techniques 206 Post-Translational Modification Prediction 207 Protein sorting 208 Proteolytic cleavage 210 Glycosylation 211 Phosphorylation 211 Chapter Summary 212 Readings for Greater Depth 213 Questions and Problems 214 Glossary 215 Solutions to Odd-Numbered Questions and Problems 217 Index 239