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Index A a-helix, 242-248, 254
Adenine (A), 8, 9, 99
Algorithms, 35-36, 84-86, 87
approximate pattern matching, 78-79
difference measures, 72-73
dynamic programming, 60-64, 78, 82, 84, 85, 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
b-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
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Index A a-helix, 242-248, 254
Adenine (A), 8, 9, 99
Algorithms, 35-36, 84-86, 87
approximate pattern matching, 78-79
difference measures, 72-73
dynamic programming, 60-64, 78, 82, 84, 85, 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
b-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
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Chirality, 213-215
Chromosomal walking, 17, 18, 42, 43
Clones and cloning, 13, 14, 26, 42-43, 209
Closed circular DNA, 153-154, 155, 156, 157, 181, 204
Coalescent, 117, 119-121
combinatorial structures, 119, 136-148
Ewens sampling formula, 119, 122-124, 136-139
K-allele model, 130-132
likelihood methods, 146-148
tree construction and movement, 124-127
see also, Finitely-many-sites model; Infinitely-many-sites model
Codons, 12, 115, 239
Colon cancer, 34, 37-42
Combinatorics, 119, 136-148, 185
Computing time and memory capacity
algorithmic efficiencies, 35-36, 84-86, 87
approximate pattern matching, 79, 87
dynamic programming algorithms, 62-63, 64, 68, 83, 84
gap cost functions, 72
heuristic algorithms, 83-84
K-best paths, 77
multiple alignments, 75
parallel processing, 79-81, 84
sublinear similarity searches, 84-85
Consecutive ones property, 50
Consensus scores, 76
Contigs, 47-50
Crick and Watson model, 153, 204-205
Crossovers, 27-29
Cruciforms, 154
Crystallography, 202, 203, 240
Cystic fibrosis (CF), 16-18, 20-21, 26
Cytosine (C), 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 FASTA, 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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technology; Strand separation and unwinding; Supercoiling
DNA polymerases, 8, 16, 154
DNA polymorphisms and mutations, 8-9, 16-17, 26, 30, 34, 57, 106
in evolutionary analysis, 114-135
as markers, 31, 34
minimal cost alignments, 72-73
in mitochondria, 115-116, 117, 118, 148-149
rates of, 66, 67, 116, 117, 124-125
see also Genetic maps and mapping
Dot plots, 68, 70
Duplex unwinding elements (DUEs), 183, 194, 195
Dynamic programming algorithm, 60-64, 78, 82, 84, 85, 86, 109, 251
E Edit graphs, 59-61, 68-70, 75
Effective population size, 117
Efficient algorithms, 35-36, 84-86, 87
Electron microscopy, 202, 211, 227
Electrostatic interactions, 251
Energetics, 154, 180, 182, 186-195
Enzymes, 3, 7, 180, 238.
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), 37-38
FASTA algorithm, 82, 83, 84
Fingerprinting methods, 42-47
Finitely-many-sites model, 132-135
Fleming-Viot process, 148
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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 Haldane 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-sites/alleles
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model, 122, 124, 125, 127-130
In vitro assays, 3
Isomerases, 238
K K-allele model, 130-132
K-best alignments, 76-78
kDNA (kinetoplast DNA), 231
Kingman's subadditive ergodic theorem, 97
Knot theory, 212
see also Tangles and knots
L Large Deviation Theory of Diffusion Processes, 37-42
Levenshtein measure, 73, 87
LexA binding sites, 198-199
Ligases, 13
Likelihood methods, 34-42, 146-148
Linear DNA, 155, 156
Linking number (Lk), 155, 157-158, 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
and 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 neoplasia) trait, 38-39
Mirror images, 213-215
Mismatch ratio, 86
Mitochondrial DNA (mtDNA), 115-116, 117, 118, 135, 148-149, 204
Molecular biology, overview, 7-12
Möbius, 143, 181
Monte Carlo methods, 146-147, 149, 241
Morgans, 28
mRNA (messenger RNA), 9, 12, 92
Multiple alignments, 73-76
Multiple minima problem, 241
Mutation, see DNA polymorphisms and mutations
Myoglobin, 265-266
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N Native American population studies, 116, 117
Neighborhood concept, 83
Neural networks, 259-263
Nonadditive scoring schemes, 87
Nuclear magnetic resonance (NMR), 203, 240
Nucleic acids, 3
Nucleosomes, 154, 166, 174-177
Nucleotides, 8, 57, 118, 204
distances, 29, 81
O Oncogenes, 58, 91, 196
Ornstein-Uhlenbeck process, 41
Overwinding, 154
P Packing density, 252
Palindromes, 87
Papilloma virus, 196, 199-200
Parallel computing, 79-81, 84, 87
Penetrance, 31, 33, 35
Phenocopy, 34
Phenotype, 38, 40
Phylogeny, 73, 76, 87
see also evolutionary trees
Physical maps and mapping, 17, 19, 26, 29
fingerprinting methods, 42-47
PIR database, 81
PLANS (Pattern Language for Amino and Nucleic Acids Sequences), 263-264
Platelet-derived growth factor (PDGF), 91
Plectonemic forms, 154, 156, 169, 170, 215-216
Poisson distributions, 144
see also Boltzmann equation, 254;
Dirichlet distribution, 144
in coalescent trees, 121, 124-127
in sequence comparisons, 29, 100-104, 108-110
Poly-adenylation, 196
Polygenic inheritance, 34
Polymerase chain reaction (PCR), 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), 99, 117, 200
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Pyrimidines (Y), 99, 117, 118, 123, 128, 200
Q QUEST systems, 87
R Rational tangles, 218-221, 228-229
RecA binding, 198-199, 211, 227
Recessive traits, 16
Recombinant DNA technology, 13-16, 17
Recombination, 27-28, 205, 213, 225-230
frequency, 28-30, 31, 35
site-specific, 207-212, 222-225
Replication processes, 92, 154, 179-180, 183, 204
Resolvase, 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), 46, 47-53
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Sequencing methods and technology, 13, 17, 19, 26, 81
error detection and correction, 73
shotgun method, 43-44
Sex chromosomes, 26
Shotgun method, 43-44
SIMD (single-instruction, multiple-data) computers, 80
Site-specific recombination, 207-212, 222-225
Smith-Waterman algorithm, 66, 68, 83, 84, 109
Solvent-accessible contact areas, 252-253
SOS genes, response, 183, 198-199, 200
Statistics of coverage, 46-51
Stochastic processes, 26, 48
coalescent structures, 119-135, 148-149
combinatorial structures, 119, 136-148
likelihood methods, 146-148
Storage capacities, see Computing time and memory capacity
Strand separation and unwinding, 8, 179-180, 181-184, 219-220
energy states, 154, 180, 182, 186-195
site prediction, 184-186, 196-200
Stress responses, 183, 198-199, 200, 204
Strong law of large numbers (SLLN), 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 (Slk), 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), 8, 99
Topology, 155, 166-167, 168, 170-171, 203-204, 205, 207, 244, 247
of strand separation, 180, 181-184, 219-220
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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
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Representative terms from entire chapter:
sequence similarity
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