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INDEX 277 Index A ARIADNE systems, 87 α-helix, 242-248, 254 Assay techniques, 2-3 Adenine (A), 8, 9, 99 Autosomes, 26 Algorithms, 35-36, 84-86, 87 B approximate pattern matching, 78-79 difference measures, 72-73 Base pairs, 8, 26, 48, 153, 154, 163, 179, 185, 188, 189, 191, dynamic programming, 60-64, 78, 82, 84, 85, 86, 109 194, 204, 249 in evolutionary analysis, 106, 110-112 see also Adenine, Thymine, Cystosine, Guanine, Uracil gap cost penalties, 70-72 Bayesian statistics, 35 in genetic mapping, 35-36 β-sheet, 242-248, 254 global alignment, 58-64, 94-99 Bernoulli random variables, 102, 125 heuristic, 82-84 Biochemistry, 2-5 K-best alignments, 76-78 Biosequences, see Databases of DNA sequences; local alignment, 65-70, 99-106 Sequence similarity and comparison; multiple alignments, 73-76 Sequencing methods and technology in physical mapping, 46-51 BLASTA algorithm, 82-84 Alleles, 6 Booth-Leuker algorithm, 50-51 Amino acids, 4, 57 BRCA1 (breast cancer) gene, 33 see also DNA; Protein folding; C Sequence similarity and comparison Cancer, 33, 34, 37-42, 58, 91, 183, 196 Amplification, see Polymerase chain reaction Catenanes, 205, 212 Ancestry, see Evolutionary analysis Cauchy's formula, 136 ANREP systems, 87 Cellular structures, 9 Antidiagonals, 62, 79-80 Chaperonins, 238-239 APC gene, 34, 37-38 Chen-Stein method, 102, 106, 110 Approximate pattern matching, 78-79, 86 Chimeras, 51 Approximate repeats, 87
INDEX 278 Chirality, 213-215 Consensus scores, 76 Chromosomal walking, 17, 18, 42, 43 Contigs, 47-50 Clones and cloning, 13, 14, 26, 42-43, 209 Crick and Watson model, 153, 204-205 Closed circular DNA, 153-154, 155, 156, 157, 181, 204 Crossovers, 27-29 Coalescent, 117, 119-121 Cruciforms, 154 combinatorial structures, 119, 136-148 Crystallography, 202, 203, 240 Ewens sampling formula, 119, 122-124, 136-139 Cystic fibrosis (CF), 16-18, 20-21, 26 K-allele model, 130-132 Cytosine (C), 8, 9, 99 likelihood methods, 146-148 tree construction and movement, 124-127 D see also, Finitely-many-sites model; Databases of DNA sequences, 13, 17, 56, 81, 87 Infinitely-many-sites model similarity searches in, 78-79, 82-86, 87, 91-92, 94 Codons, 12, 115, 239 see also FASTA, BLASTA Colon cancer, 34, 37-42 Dayhoff matrix, 66, 67, 83 Combinatorics, 119, 136-148, 185 Diagnostics, see Genetic diagnostics Computing time and memory capacity Difference measures, 72-73 algorithmic efficiencies, 35-36, 84-86, 87 Diffusion processes, 37-42, 148 approximate pattern matching, 79, 87 Dimers, 212 dynamic programming algorithms, 62-63, 64, 68, 83, 84 DNA (deoxyribonucleic acid), 8-9, 92 gap cost functions, 72 primers, 13, 15, 16 heuristic algorithms, 83-84 protein binding, 166-167, 168, 170-171, 181 K-best paths, 77 transcription, 9-12, 154, 179, 196-198, 204-205 multiple alignments, 75 see also DNA polymorphisms and mutations; parallel processing, 79-81, 84 Protein folding; sublinear similarity searches, 84-85 Sequence similarity and comparison; Consecutive ones property, 50 Sequencing methods and technology;
INDEX 279 Strand separation and unwinding; Eve hypothesis, 116 Supercoiling Evolutionary analysis, 57-58, 90-94 DNA polymerases, 8, 16, 154 coalescent structures, 117, 119-135, 148-149 DNA polymorphisms and mutations, 8-9, 16-17, 26, 30, 34, common origins, 57, 248 57, 106 extremal statistical methods, 106-112 in evolutionary analysis, 114-135 minimal cost alignments, 72-73 as markers, 31, 34 multiple alignments, 73, 76 minimal cost alignments, 72-73 random combinatorial structures, 136-148 in mitochondria, 115-116, 117, 118, 148-149 use of mitochondrial DNA, 57-58, 90-94, 115-116, 117, rates of, 66, 67, 116, 117, 124-125 148-149 see also Genetic maps and mapping trees, 73, 76, 87, 124, 129, 132, 266 Dot plots, 68, 70 see also Eve hypothesis Duplex unwinding elements (DUEs), 183, 194, 195 Ewens sampling formula (ESF), 119, 122-124, 136-139 Dynamic programming algorithm, 60-64, 78, 82, 84, 85, 86, Extremal statistical methods, 106-112 109, 251 global sequence comparisons, 94-99 local sequence comparisons, 99-106 E Edit graphs, 59-61, 68-70, 75 F Effective population size, 117 False negatives and positives, 51 Efficient algorithms, 35-36, 84-86, 87 Familial adenomatous polyopsis (FAP), 37-38 Electron microscopy, 202, 211, 227 FASTA algorithm, 82, 83, 84 Electrostatic interactions, 251 Fingerprinting methods, 42-47 Energetics, 154, 180, 182, 186-195 Finitely-many-sites model, 132-135 Enzymes, 3, 7, 180, 238. Fleming-Viot process, 148 see also under names of specific types
INDEX 280 Foldases, 237-238 Global alignment, 5, 58-64, 94-99 Fourier transforms, coefficient, 240 maximum-scoring, 63 4-plat knots, 215-216, 220, 222 Graph theory, 46, 51 Fractionation, 2-3 Guanine (G), 8, 9, 99 Free energy, 154, 180, 182, 186-195 H G Haldane mapping function, 29, 41 Gap costs, 70-72, 77-78 Hierarchical condensation methods, 248-251 Gaussian processes, 41 Helix, 8, 9, 153 Gel electrophoresis, 210-211, 227 destabilization, 184, 188, 196 GENBANK database, 81 Helical periodicity, 154 Generalized Levenshtein measure, 73, 87 Heterozygotes, 6, 16, 31 Gene splicing, see Recombinant DNA technology Heuristic algorithms, 82-84 Gene therapy, 18 Histones, 154, 175 Genetic code, 12, 239 HIV protease structure, 254-255 Genetic diagnostics, 16, 17 Homeomorphisms, 212-213 Genetic distance, 28-29 Homology modeling, 252 Genetic heterogeneity, 34 Homozygotes, 6, 31 Genetic maps and mapping, 16, 18-19, 26, 27-30, 51 Human Genome Project, 18-22, 26 and incomplete pedigree information, 30, 31, 34-35 Hydrophilic side chains, 244, 253, 263 markers in, 31 Hydrophobic side chains, 244, 245, 253 and maximum likelihood estimation, 34-42 Hydrophobicity, 4 and non-Mendelian genetics, 30, 31, 33-34 Genetic markers, 31, 34, 42 I Genetics, 5-7 Incomplete penetrance, 31, 33, 34 Genotype, 38, 40 Independent assortment, 29 Geometry, 166, 203, 210, 211, 220, 223 Indexing, of databases, 87 descriptors and methods, 155-163 Infinitely-many-sites/alleles see also Topology
INDEX 281 model, 122, 124, 125, 127-130 Mapping, see Genetic maps and mapping; In vitro assays, 3 Physical maps and mapping; Isomerases, 238 Restriction maps; Sequencing methods and technology K Markers, see Genetic markers K-allele model, 130-132 Markov models, processes, 36, 146-147, 249 K-best alignments, 76-78 Maximum likelihood estimation, 34-35 kDNA (kinetoplast DNA), 231 and efficient algorithms, 35-36 Kingman's subadditive ergodic theorem, 97 and statistical significance, 37-42 Knot theory, 212 Measure-valued diffusions, 148 see also Tangles and knots Membrane-bound transporters, 17-18, 20 Mendelian genetics, 5-7, 27, 31 L Minichromosomes, 174-177 Large Deviation Theory of Diffusion Processes, 37-42 Min (multiple intestinal neoplasia) trait, 38-39 Levenshtein measure, 73, 87 Mirror images, 213-215 LexA binding sites, 198-199 Mismatch ratio, 86 Ligases, 13 Mitochondrial DNA (mtDNA), 115-116, 117, 118, 135, Likelihood methods, 34-42, 146-148 148-149, 204 Linear DNA, 155, 156 Molecular biology, overview, 7-12 Linking number (Lk), 155, 157-158, 163-164, 173-174, 181 Möbius, 143, 181 minichromosomes, 175, 177 Monte Carlo methods, 146-147, 149, 241 surface, 167-171, 173-174 Morgans, 28 topoisomerase reactions, 164-166 mRNA (messenger RNA), 9, 12, 92 Local alignment, 5, 65-70, 99-106 Multiple alignments, 73-76 Longest common subsequence, 99 Multiple minima problem, 241 Mutation, see DNA polymorphisms and mutations M Myoglobin, 265-266 Macromolecules, 3
INDEX 282 N PLANS (Pattern Language for Amino and Nucleic Acids Native American population studies, 116, 117 Sequences), 263-264 Neighborhood concept, 83 Platelet-derived growth factor (PDGF), 91 Neural networks, 259-263 Plectonemic forms, 154, 156, 169, 170, 215-216 Nonadditive scoring schemes, 87 Poisson distributions, 144 Nuclear magnetic resonance (NMR), 203, 240 see also Boltzmann equation, 254; Nucleic acids, 3 Dirichlet distribution, 144 Nucleosomes, 154, 166, 174-177 in coalescent trees, 121, 124-127 Nucleotides, 8, 57, 118, 204 in sequence comparisons, 29, 100-104, 108-110 distances, 29, 81 Poly-adenylation, 196 Polygenic inheritance, 34 O Polymerase chain reaction (PCR), 13, 15, 16, 46 Polymorphism, see DNA polymorphisms and mutations Oncogenes, 58, 91, 196 Polyoma virus, 196 Ornstein-Uhlenbeck process, 41 Primers, 13, 15, 16 Overwinding, 154 Principle of optimality, 63 P Probabilistic combinatorics, 136 Processing time, see Computing time and memory capacity Packing density, 252 Protein folding, 5, 12, 236-248 Palindromes, 87 hierarchical condensation methods, 248-251, 256-265 Papilloma virus, 196, 199-200 prediction of, 5, 254-255, 265-266 Parallel computing, 79-81, 84, 87 threading methods, 248-254 Penetrance, 31, 33, 35 Proteins, 3-5, 7-8, 57, 92 Phenocopy, 34 see also Amino acids; Phenotype, 38, 40 Protein folding; Phylogeny, 73, 76, 87 Sequence similarity and comparison see also evolutionary trees Public databases, see Databases of DNA sequences Physical maps and mapping, 17, 19, 26, 29 Pure breeding, 5 fingerprinting methods, 42-47 Purines (R), 99, 117, 200 PIR database, 81
INDEX 283 Pyrimidines (Y), 99, 117, 118, 123, 128, 200 Scoring schemes gap cost penalties, 70-72 Q global alignments, 59-64 QUEST systems, 87 K-best alignments, 76-78 local alignments, 65-68 R minimal cost alignments, 72-73 Rational tangles, 218-221, 228-229 multiple alignments, 74-76 RecA binding, 198-199, 211, 227 nonadditive, 87 Recessive traits, 16 unit-cost, 58-59, 86 Recombinant DNA technology, 13-16, 17 Sedimentation rate, 100 Recombination, 27-28, 205, 213, 225-230 Self-replication, 92 frequency, 28-30, 31, 35 Sequence similarity and comparison, 56-58, 86-87, 91, 199 site-specific, 207-212, 222-225 approximate pattern matching, 78-79, 86 Replication processes, 92, 154, 179-180, 183, 204 database searches, 78-79, 82-86, 87, 91-92, 94 Resolvase, 213, 225-230 difference measures, 72-73 Restriction enzymes, 13 in evolutionary analysis, 57-58, 72-73, 76, 90-94, 106-112, Restriction fragment lists, 45-46 115 Restriction maps, 44-45, 87 gap cost penalties, 70-72 R-group, 237 global alignment, 5, 58-64, 94-99 Ribosomes, 9, 10, 12, 92 heuristic algorithms, 82-84 RNA (ribonucleic acid), 9, 179, 196, 237 K-best alignments, 76-78 evolutionary analysis, 92-93, 106-107, 110-112 local alignment, 5, 65-70, 99-106 polymerase, 9 multiple alignments, 73-76 rRNA, 92, 93, 106, 107, 110, 112 parallel computing, 79-81, 84, 87 see also mRNA, tRNA, 11 sublinear, 84-86 Rule-based methods, 263-264 Sequence tagged sites (STSs), 46, 47-53 S
INDEX 284 Sequencing methods and technology, 13, 17, 19, 26, 81 Sum-of-pairs scores, 76 error detection and correction, 73 Supercoiling processes, 153-163 shotgun method, 43-44 closed curves, 153-154, 155, 156, 157, 181, 204 Sex chromosomes, 26 nucleosomes, 154, 174-177 Shotgun method, 43-44 topoisomerase reactions, 163-166 SIMD (single-instruction, multiple-data) computers, 80 see also Strand separation and unwinding; Site-specific recombination, 207-212, 222-225 Superhelicity Smith-Waterman algorithm, 66, 68, 83, 84, 109 Superhelicity, 162, 181-183, 193 Solvent-accessible contact areas, 252-253 Surface linking number (Slk), 167-171, 173-174 SOS genes, response, 183, 198-199, 200 Synapsis, 207-209, 223-225, 226-227 Statistics of coverage, 46-51 Systolic arrays, 80-81, 83-84 Stochastic processes, 26, 48 coalescent structures, 119-135, 148-149 T combinatorial structures, 119, 136-148 Tangles and knots, 204-207, 211, 212-222 likelihood methods, 146-148 gel mobility, 231-232 Storage capacities, see Computing time and memory capacity recognition, 230-231 Strand separation and unwinding, 8, 179-180, 181-184, site-specific recombination models, 222-225 219-220 Threading methods, 248-254 energy states, 154, 180, 182, 186-195 Thymine (T), 8, 99 site prediction, 184-186, 196-200 Topology, 155, 166-167, 168, 170-171, 203-204, 205, 207, Stress responses, 183, 198-199, 200, 204 244, 247 Strong law of large numbers (SLLN), 97, 98, 100 of strand separation, 180, 181-184, 219-220 Sublinear similarity searches, 84-86
INDEX 285 surface linking number, 167-171, 173-174 tangles and knots, 204-207, 211, 212-225, 230-231 see also Geometry Topoisomerase, 164-166, 175 Toroidal surfaces, 155, 168, 170, 182, 228-229, 231 Traceback procedures, 64 Transcription processes, 9-12, 154, 179, 196-198, 204-205 Transitions, 117, 185-186, 188, 190, 194-195 Trivial tangles, 218-219 tRNA (transfer RNA), 92, 93, 106, 107, 110-112 t-test, 40-41 Twist (Tw), 157, 159-160, 162, 164, 173-174 topoisomerase reactions, 164-166 U Underwinding, 154, 164 Unit-cost scoring scheme, 58-59, 86 Unwinding, see Strand separation and unwinding Uracil (U), 9, 12 V Variable population size processes, 148-149 Virtual surfaces, 17-171 Vitalism, 3 VLSI (very large scale integration) chips, 80-81 v-sis oncogene, 58, 91 W Winding number, 167, 171-172, 173-174 Writhe (Wr), 157, 159, 160, 161, 162, 164 topoisomerase reactions, 164-166 X X-ray crystallography, 203, 240 Y YAC (yeast artificial chromosomes) libraries, 46-47, 53 Z z-DNA, 154
