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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