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From page 277... ... 86, 109 in evolutionary analysis, 106, 110-112 gap cost penalties, 70-72 in genetic mapping, 35-36 global alignment, 58-64, 94-99 heuristic, 82-84 K-best alignments, 76-78 local alignment, 65-70, 99-106 multiple alignments, 73-76 in physical mapping, 46-51 Alleles, 6 Amino acids, 4, 57 see also DNA; Protein folding; Sequence similarity and comparison Amplification, see Polymerase chain reaction Ancestry, see Evolutionary analysis ANREP systems, 87 Antidiagonals, 62, 79-80 APC gene, 34,37-38 Approximate pattern matching, 78-79, 86 Approximate repeats, 87 ARIADNE systems, 87 Assay techniques, 2-3 Autosomes, 26 B Base pairs, 8, 26, 48, 153, 154, 163, 179, 185, 188, 189, 191, 194, 204, 249 see also Adenine, Thymine, Cystosine, Guanine, Uracil Bayesian statistics, 35 ,8-sheet, 242-248, 254 Bernoulli random variables, 102, 125 Biochemistry, 2-5 Biosequences, see Databases of DNA sequences; Sequence similarity and comparison; Sequencing methods and technology BLASTA algorithm, 82-84 Booth-Leuker algorithm, 50-51 BRCA1 (breast cancer) gene, 33 C Cancer, 33, 34, 37-42, 58, 91, 183, 196 Catenanes, 205, 212 Cauchy's formula, 136 Cellular structures, 9 Chaperonins, 238-239 Chen-Stein method, 102, 106, 110 Chimeras 51 277 Read the entire page →
From page 278... ... , 8, 9, 99 D Databases of DNA sequences, 13, 17, 56, 81, 87 similarity searches in, 78-79, 82-86, 87, 91-92, 94 see also PASTA, BLASTA Dayhoff matrix, 66, 67, 83 Diagnostics, see Genetic diagnostics Difference measures, 72-73 Diffusion processes, 37-42, 148 Dimers, 212 DNA (deoxyribonucleic acid) , 8-9, 92 primers, 13, 15, 16 protein binding, 166- 167, 168, 170-171, 181 transcription, 9-12, 154, 179, 196-198, 204-205 see also DNA polymorphisms and mutations; Protein folding; Sequence similarity and comparison; Sequencing methods and Read the entire page →
From page 279... ... see also under names of specific types Eve hypothesis, 116 Evolutionary analysis, 57-58, 90-94 coalescent structures, 117, 119-135, 148-149 common origins, 57, 248 extremal statistical methods 106-112 minimal cost alignments, 72-73 multiple alignments, 73, 76 random combinatorial structures, 136-148 use of mitochondrial DNA, 57-58, 90-94, 115-116, 117, 148-149 trees, 73, 76, 87, 124, 129, 132, 266 see also Eve hypothesis Ewens sampling formula (ESF) , 119, 122-124, 136-139 Extremal statistical methods, 106-112 global sequence comparisons, 94-99 local sequence comparisons, 99-106 F False negatives and positives, 51 Familial adenomatous polyopsis (FAP) Read the entire page →
From page 280... ... 280 CALCULATING THE SECRETS OF LIFE Foldases, 237-238 Fourier transforms, coefficient' 240 4-plat knots, 215-216, 220, 222 Fractionation, 2-3 Free energy, 154, 180, 182, 186-195 G Gap costs, 70-72, 77-78 Gaussian processes, 41 Gel electrophoresis, 210-211, 227 GENBANK database, 81 Generalized Levenshtein measure, 73, 87 Gene splicing, see Recombinant DNA technology Gene therapy, 18 Genetic code, 12, 239 Genetic diagnostics, 16, 17 Genetic distance, 28-29 Genetic heterogeneity, 34 Genetic maps and mapping, 16, 18-19, 26, 27-30, 51 and incomplete pedigree information, 30, 31, 34-35 markers in, 31 and maximum likelihood estimation, 34-42 and non-Mendelian genetics, 30,31, 33-34 Genetic markers, 31, 34, 42 Genetics, 5-7 Genotype, 38, 40 Geometry, 166, 203, 210, 211, 220, 223 descriptors and methods, 155-163 see also Topology Global alignment, 5, 58-64, 94-99 maximum-scoring, 63 Graph theory, 46, 51 Guanine (G) , 8, 9, 99 H HaIdane mapping function, 29, 41 Hierarchical condensation methods, 248-251 Helix, 8, 9, 153 destabilization, 184, 188, 196 Helical periodicity, 154 Heterozygotes, 6, 16,31 Heuristic algorithms, 82-84 Histones, 154, 175 HIV protease structure, 254-255 Homeomorphisms, 212-213 Homology modeling, 252 Homozygotes, 6,31 Human Genome Project, 18-22, 26 Hydrophilic side chains, 244, 253, 263 Hydrophobic side chains, 244, 245, 253 Hydrophobicity, 4 I Incomplete penetrance, 31, 33, 34 Independent assortment, 29 Indexing, of databases, 87 Infinitely-many- site s/allele s Read the entire page →
From page 281... ... , 155, 157-15S, 163-164, 173-174, 181 minichromosomes, 175, 177 surface, 167-171, 173-174 topoisomerase reactions, 164-166 Local alignment, 5, 65-70, 99-106 Longest common subsequence, 99 M Macromolecules, 3 Mapping, see Genetic maps and mapping; Physical maps and mapping; Restriction maps; Sequencing methods and technology Markers, see Genetic markers Markov models, processes, 36, 146-147, 249 Maximum likelihood estimation, 34-35 and efficient algorithms, 35-36 ant! statistical significance, 37-42 Measure-valued diffusions, 148 Membrane-bound transporters, 17-18, 20 Mendelian genetics, 5-7, 27, 31 Minichromosomes, 174- 177 Min (multiple intestinal neo plasia) Read the entire page →
From page 282... ... , 13, 15, 16, 46 Polymorphism, see DNA polymorphisms and mutations Polyoma virus, 196 Primers, 13, 15, 16 Principle of optimality, 63 Probabilistic combinatorics, 136 Processing time, see Computing time and memory capacity Protein folding, 5, 12, 236-248 hierarchical condensation methods, 248-251, 256-265 prediction of 5, 254-255, 265-266 threading methods, 248-254 Proteins, 3-5, 7-8, 57, 92 see also Amino acids; Protein folding; Sequence similarity and comparison Public databases, see Databases of DNA sequences Pure breeding, 5 Purines (R) Read the entire page →
From page 283... ... 213, 225-230 Restriction enzymes, 13 Restriction fragment lists, 45-46 Restriction maps, 44-45, 87 R-group, 237 Ribosomes, 9, 10, 12, 92 RNA (ribonucleic acid) , 9, 179, 196, 237 evolutionary analysis, 92-93, 106-107, 110-112 polymerase, 9 rRNA, 92, 93, 106, 107, 110, 112 see also mRNA, tRNA, 11 Rule-based methods, 263-264 S Scoring schemes gap cost penalties, 70-72 global alignments, 59-64 K-best alignments, 76-78 local alignments, 65-68 minimal cost alignments, 72-73 multiple alignments, 74-76 nonadditive, 87 unit-cost, 58-59, 86 Sedimentation rate, 100 Self-replication, 92 Sequence similarity and comparison, 56-58, 86-87 91, 199 approximate pattern matching, 78-79, 86 database searches, 78-79, 82-86, 87, 91-92, 94 difference measures, 72-73 in evolutionary analysis, 57-58, 72-73, 76, 90-94, 106-112, 115 gap cost penalties, 70-72 global alignment, 5, 58-64, 94-99 heuristic algorithms, 82-84 K-best alignments, 76-78 local alignment, 5, 65-70, 99-106 multiple alignments, 73-76 parallel computing, 79-81, 84, 87 sublinear, 84-86 Sequence tagged sites (STSs) Read the entire page →
From page 284... ... , 97, 98, 100 Sublinear similarity searches, 84-86 Sum-of-pairs scores, 76 Supercoiling processes, 153-163 closed curves, 153- 154, 155, 156, 157, 181, 204 nucleosomes, 154, 174-177 topoisomerase reactions, 163-166 see also Strand separation and unwinding; Superhelicity Superhelicity, 162, 181- 183, 193 Surface linking number (SZk) , 167-171, 173-174 Synapsis, 207-209, 223-225, 226-227 Systolic arrays, 80-81, 83-84 T Tangles and knots, 204-207, 211, 212-222 gel mobility, 231-232 recognition, 230-231 site-specific recombination models, 222-225 Threading methods, 248-254 Thymine (T) Read the entire page →
From page 285... ... , 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 UraciT (u) , 9, 12 V Variable population size processes, 148-149 Virtual surfaces, 17-171 Vitalism, 3 VLSI (very large scale integration) Read the entire page →

From page 277...

... 86, 109 in evolutionary analysis, 106, 110-112 gap cost penalties, 70-72 in genetic mapping, 35-36 global alignment, 58-64, 94-99 heuristic, 82-84 K-best alignments, 76-78 local alignment, 65-70, 99-106 multiple alignments, 73-76 in physical mapping, 46-51 Alleles, 6 Amino acids, 4, 57 see also DNA; Protein folding; Sequence similarity and comparison Amplification, see Polymerase chain reaction Ancestry, see Evolutionary analysis ANREP systems, 87 Antidiagonals, 62, 79-80 APC gene, 34,37-38 Approximate pattern matching, 78-79, 86 Approximate repeats, 87 ARIADNE systems, 87 Assay techniques, 2-3 Autosomes, 26 B Base pairs, 8, 26, 48, 153, 154, 163, 179, 185, 188, 189, 191, 194, 204, 249 see also Adenine, Thymine, Cystosine, Guanine, Uracil Bayesian statistics, 35 ,8-sheet, 242-248, 254 Bernoulli random variables, 102, 125 Biochemistry, 2-5 Biosequences, see Databases of DNA sequences; Sequence similarity and comparison; Sequencing methods and technology BLASTA algorithm, 82-84 Booth-Leuker algorithm, 50-51 BRCA1 (breast cancer) gene, 33 C Cancer, 33, 34, 37-42, 58, 91, 183, 196 Catenanes, 205, 212 Cauchy's formula, 136 Cellular structures, 9 Chaperonins, 238-239 Chen-Stein method, 102, 106, 110 Chimeras 51 277

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From page 278...

... , 8, 9, 99 D Databases of DNA sequences, 13, 17, 56, 81, 87 similarity searches in, 78-79, 82-86, 87, 91-92, 94 see also PASTA, BLASTA Dayhoff matrix, 66, 67, 83 Diagnostics, see Genetic diagnostics Difference measures, 72-73 Diffusion processes, 37-42, 148 Dimers, 212 DNA (deoxyribonucleic acid) , 8-9, 92 primers, 13, 15, 16 protein binding, 166- 167, 168, 170-171, 181 transcription, 9-12, 154, 179, 196-198, 204-205 see also DNA polymorphisms and mutations; Protein folding; Sequence similarity and comparison; Sequencing methods and

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From page 279...

... see also under names of specific types Eve hypothesis, 116 Evolutionary analysis, 57-58, 90-94 coalescent structures, 117, 119-135, 148-149 common origins, 57, 248 extremal statistical methods 106-112 minimal cost alignments, 72-73 multiple alignments, 73, 76 random combinatorial structures, 136-148 use of mitochondrial DNA, 57-58, 90-94, 115-116, 117, 148-149 trees, 73, 76, 87, 124, 129, 132, 266 see also Eve hypothesis Ewens sampling formula (ESF) , 119, 122-124, 136-139 Extremal statistical methods, 106-112 global sequence comparisons, 94-99 local sequence comparisons, 99-106 F False negatives and positives, 51 Familial adenomatous polyopsis (FAP)

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From page 280...

... 280 CALCULATING THE SECRETS OF LIFE Foldases, 237-238 Fourier transforms, coefficient' 240 4-plat knots, 215-216, 220, 222 Fractionation, 2-3 Free energy, 154, 180, 182, 186-195 G Gap costs, 70-72, 77-78 Gaussian processes, 41 Gel electrophoresis, 210-211, 227 GENBANK database, 81 Generalized Levenshtein measure, 73, 87 Gene splicing, see Recombinant DNA technology Gene therapy, 18 Genetic code, 12, 239 Genetic diagnostics, 16, 17 Genetic distance, 28-29 Genetic heterogeneity, 34 Genetic maps and mapping, 16, 18-19, 26, 27-30, 51 and incomplete pedigree information, 30, 31, 34-35 markers in, 31 and maximum likelihood estimation, 34-42 and non-Mendelian genetics, 30,31, 33-34 Genetic markers, 31, 34, 42 Genetics, 5-7 Genotype, 38, 40 Geometry, 166, 203, 210, 211, 220, 223 descriptors and methods, 155-163 see also Topology Global alignment, 5, 58-64, 94-99 maximum-scoring, 63 Graph theory, 46, 51 Guanine (G) , 8, 9, 99 H HaIdane mapping function, 29, 41 Hierarchical condensation methods, 248-251 Helix, 8, 9, 153 destabilization, 184, 188, 196 Helical periodicity, 154 Heterozygotes, 6, 16,31 Heuristic algorithms, 82-84 Histones, 154, 175 HIV protease structure, 254-255 Homeomorphisms, 212-213 Homology modeling, 252 Homozygotes, 6,31 Human Genome Project, 18-22, 26 Hydrophilic side chains, 244, 253, 263 Hydrophobic side chains, 244, 245, 253 Hydrophobicity, 4 I Incomplete penetrance, 31, 33, 34 Independent assortment, 29 Indexing, of databases, 87 Infinitely-many- site s/allele s

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From page 281...

... , 155, 157-15S, 163-164, 173-174, 181 minichromosomes, 175, 177 surface, 167-171, 173-174 topoisomerase reactions, 164-166 Local alignment, 5, 65-70, 99-106 Longest common subsequence, 99 M Macromolecules, 3 Mapping, see Genetic maps and mapping; Physical maps and mapping; Restriction maps; Sequencing methods and technology Markers, see Genetic markers Markov models, processes, 36, 146-147, 249 Maximum likelihood estimation, 34-35 and efficient algorithms, 35-36 ant! statistical significance, 37-42 Measure-valued diffusions, 148 Membrane-bound transporters, 17-18, 20 Mendelian genetics, 5-7, 27, 31 Minichromosomes, 174- 177 Min (multiple intestinal neo plasia)

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From page 282...

... , 13, 15, 16, 46 Polymorphism, see DNA polymorphisms and mutations Polyoma virus, 196 Primers, 13, 15, 16 Principle of optimality, 63 Probabilistic combinatorics, 136 Processing time, see Computing time and memory capacity Protein folding, 5, 12, 236-248 hierarchical condensation methods, 248-251, 256-265 prediction of 5, 254-255, 265-266 threading methods, 248-254 Proteins, 3-5, 7-8, 57, 92 see also Amino acids; Protein folding; Sequence similarity and comparison Public databases, see Databases of DNA sequences Pure breeding, 5 Purines (R)

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From page 283...

... 213, 225-230 Restriction enzymes, 13 Restriction fragment lists, 45-46 Restriction maps, 44-45, 87 R-group, 237 Ribosomes, 9, 10, 12, 92 RNA (ribonucleic acid) , 9, 179, 196, 237 evolutionary analysis, 92-93, 106-107, 110-112 polymerase, 9 rRNA, 92, 93, 106, 107, 110, 112 see also mRNA, tRNA, 11 Rule-based methods, 263-264 S Scoring schemes gap cost penalties, 70-72 global alignments, 59-64 K-best alignments, 76-78 local alignments, 65-68 minimal cost alignments, 72-73 multiple alignments, 74-76 nonadditive, 87 unit-cost, 58-59, 86 Sedimentation rate, 100 Self-replication, 92 Sequence similarity and comparison, 56-58, 86-87 91, 199 approximate pattern matching, 78-79, 86 database searches, 78-79, 82-86, 87, 91-92, 94 difference measures, 72-73 in evolutionary analysis, 57-58, 72-73, 76, 90-94, 106-112, 115 gap cost penalties, 70-72 global alignment, 5, 58-64, 94-99 heuristic algorithms, 82-84 K-best alignments, 76-78 local alignment, 5, 65-70, 99-106 multiple alignments, 73-76 parallel computing, 79-81, 84, 87 sublinear, 84-86 Sequence tagged sites (STSs)

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From page 284...

... , 97, 98, 100 Sublinear similarity searches, 84-86 Sum-of-pairs scores, 76 Supercoiling processes, 153-163 closed curves, 153- 154, 155, 156, 157, 181, 204 nucleosomes, 154, 174-177 topoisomerase reactions, 163-166 see also Strand separation and unwinding; Superhelicity Superhelicity, 162, 181- 183, 193 Surface linking number (SZk) , 167-171, 173-174 Synapsis, 207-209, 223-225, 226-227 Systolic arrays, 80-81, 83-84 T Tangles and knots, 204-207, 211, 212-222 gel mobility, 231-232 recognition, 230-231 site-specific recombination models, 222-225 Threading methods, 248-254 Thymine (T)

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From page 285...

... , 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 UraciT (u) , 9, 12 V Variable population size processes, 148-149 Virtual surfaces, 17-171 Vitalism, 3 VLSI (very large scale integration)

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