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| Ïîèñê ïî óêàçàòåëÿì |
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| Clote P., Backofen R. — Computational Molecular Biology |
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| Ïðåäìåòíûé óêàçàòåëü |
 sheet 16
Absolute performance 236
Addition law 24
Additive metric 152
Additive tree metric 147
Additivity of alignments 90 95
Adenine 8
Adenoside triphosphate (ATP) 4—6
Alcohol 5
Alignment 88 90—95 97—110
Alignment, additivity 90 95
Alignment, distance 88 90 100
Alleles 11—12
Amine 5
Amino acids 6 14—15 17—
Amino acids, codes 18
Amino acids, pair potentials 35 223—228
Amino acids, pair probabilities 86—88
Amino acids, sequences 137—139
Amino acids, substitution matrix methods 139
Amino group 4 5 14:
Aminoacyl-tRNA synthetase 20 21
Amoeba dubia 12
Anchor region rules 122
Antiparallel sheets 16
Archaea 1
Archaebacteria 1
Asymptotic complexity 263
Asymptotic performance 236
Australopithecus 335
Avogadro's number 38
Back mutations 137 138
Backtrack 210
Balanced cut 239—242
Balanced state 44
Baldi — Chauvin gradient descent 187—191
Baldi — Chauvin updates 188—191
Bases, chemical forms 8
Basic U-folds 239
Baum — Welch method 180—188
Baum — Welch parameter 184
Baum — Welch score 178 179
Bayes' rule 25
Bender's theorem 205
Bernouilli random variable 27 28
Bernouilli trial 27
Bezout's Lemma 77—79
Binary phylogenetic trees 145—147
Binary trees 144 145 166
Binomial coefficients 24
Binomial distribution 27—28
Bioinformatics 2
Block structure 239—242
Block-respecting codes 56 57 59
Block-structured code 56
BLOSUM matrices 88
Boltzmann distribution 35—38 45 46 181 221
Boltzmann probability 45 46
Boltzmann probability distribution 63 64
Boltzmann's constant 38 66
Boltzmann's law 63
Boolean cellular automation 74
Box — Muller algorithm 32
Branch lengths 156—157 162—165
Branch-and-bound algorithm 249—258
Brookhaven Protein Database (PDB) 266
Cantor — Bendixson derivative 207
Carbohydrates 4
Carboxyl group 4 5 14
Carboxylic acid 5
Catalan numbers 204
CATH database 266
Cavalli — Sforza — Edwards theorem 145—147
Central limit theorem 31
Chaperones 21
Chloroplast DNA (cpDNA) 140
Chromosomal duplication 319
Chromosomal rearrangement 119
Chromosomes 9 12 60 119 233—234
Clustering methods 144—157
Codons 17
Combinatorial optimization 53—61
Combinatorial optimization, exercises 73—75
Complete maximum-weight trace (CMWT) formalization 114
Computational biology 2
Conditional likelihood 161—162
Conditional probability 25 49—50 181
Connected neighbors 229
Constraint-based structure prediction 243—246
Core Model 247—248 259
covalent bond 3
Cro Magnon 135—136
Crossover 61
Cryptogenes 120—123
Cyanobacteria 1 cytosine 8
Cytosine 8
Dempster et al. theorem 186
Deoxyribose 7
Dinucleotide entropy 67—68
Directed graph 144
Discrete Markov model 175
Distance matrix 94 154
Disulfide bonds 17
Divergence 67
DNA 2 8—12
DNA replication 21
DNA strand separation 213—223
Drosophilia 197
Duplication 119
Dynamic programming 112
Dynamic programming algorithm 107
Edit distance 88—90
Edit operation 89
Energy functions 213
Energy matrix computation 210
Enthalpy 66
entropy 61—72
Entropy, exercises 75—76
Entropy, information theoretic 62—63
Equilibrium distribution 42 45 46
Ergodic state 44
Error distance 192
Escherichia coli 1
Ester 5
Eukarya 2
Eukaryotes 1 20
Eukaryotic DNA 214
Eukaryotic DNA, promotor regions 195—197
Eukaryotic DNA, promotor sequence 196
Evolution rates 135—174
Evolution rates, change rate 137—144
Evolution rates, exercises 171—173
Expectation maximization 180
Expectation maximization algorithm 184—187
Expected number of transitions 180 182
Exponential distribution 30 33—34
Extrachromosomal element (ECE) 9
Farris transformed distance method 154
Fatty acids 4
Feller theorem 34
Fibrinopeptides 140
Fission 119
Fitch — Margoliash method 156—157
Foldicity 231
Folding 233—234
Folding point 239—242
Folding, hydrophobic force 235
Forward method 178
Forward variable, definition 178—179
Fusion 119
| Gap function 131
Gap penalty 94—95 111
Gaussian distribution 30
Geman — Geman theorem 51
Gene 11
GENEMARK 47
Genetic algorithms 60—61 233—234
genetic code 18 19
Genetic code, fault tolerant 55—60
Genetic code, optimality 55—60
Genome 11
Genomic analysis 66—68
Genomic rearrangements 318—320
Genomic segmentation algorithm 69—72
Genomic signature 68
Geometric distribution 28—29
Gibbs distribution 47—49 51
Gibbs free energy 38
Gibbs sampler 47—52 312
Global pairwise sequence alignment 88—111
Gotoh algorithm 82 100—102
Gotoh theorem 96
Gradient descent method 54 180
GU base pairs 205 209
Guanine 8
Guide RNA (gRNA) 13 20 120—123 123—128
Haemophilus influenzae 67 68
Hamming distance 205
Hart — Istrail approximation algorithm 234—242
Heteropolymer protein model 231
Hidden Markov models (HMM) 117 175—199
Hidden Markov models (HMM), applications 193—197
Hidden Markov models (HMM), exercises 197—198
Hidden Markov models (HMM), urn model 176
Homo erectus 135
Homo habilis 135
Homologous modeling 201
Homologous proteins 83—84
Homology testing 81
Hydrocarbon molecule 4
Hydrogen bonds 3 9 12
Hydrophilic amino acid 229
Hydrophilic molecules 1
Hydrophobic amino acid 229
Hydrophobic force 4 37
Hydrophobic molecules 4
Hydroxyl group 4 5
Hypergeometric distribution 32
Information (entropy) 62
Information flow 2
Information theoretic entropy 62—63
Inter-chromosomal events 119
Interaction graph 248—249
Internal energy 66
Intra-chromosomal events 119
inversion 139
Jaccard's index 76
Jensen — Shannon divergence 69—70
Kececioglu theorem 116
Kececioglu, Li, Tromp algorithm 118
Kronecker  -function 144 158
L. tarenolae 121
Lagrange multipliers 53—54 59 63 64 132 219 264
Lattice connectivity constant 236
Lattice models of proteins 228—234
Lawrence, Altschul, Boguski, Liu, Neuwald, Wootton algorithm 113
Least common ancestor 354
Likelihood 177—180
Likelihood, recursive definition 160—162
Linking number 214
Local alignments 111
Local move set 231—232
Log odds ratios 86
Majority consensus tree 170—171
Mamitsuka's MA algorithm 191—193
Mamitsuko's updates 192—193
Markov chain 38—43 127 140 141 220
Markov chain Monte Carlo algorithm 43
Markov chain, definition 176
Markov chain, irreducible 39
Markov chain, reversible 42
Markov chain, stationary 39 42
Markov matrix 141
Markov model 125
Markov model, definition 177
Markov model, order 176
Markov process 140
Markov property 140—141 176
Markov random fields 47—51
Mathematical concepts 23—79
Mathematical models 23
Maximal entropy probability distribution 65
Maximum entropy 66
Maximum Likelihood Estimation 52—53 117 157—166 184
Maximum-likelihood estimation, pair probabilities 132—133
Maximum-weight trace 114—117
Mean square difference 56
Meiosis 12 21
Messenger RNA (mRNA) 13 20 120
Methanococcus jannaschii 1 2 9 67—70 266
Methionine 21
Metric 147
Metric, definition 90
Metropolis et al. theorem 46
Metropolis — Hastings algorithm 35 37 43—47
Mitochondrial DNA (mtDNA) 136 140
Mitosis 12 21
Molecular biology, exercises 21—22
Molecular biology, overview 1—22
Molecular fossils 13
Monte Carlo algorithm 43 220
Monte Carlo applications 55—60
Moore automation 125 127
Motifs 16
Multiloops 207
Multinomial coefficients 24
Multinomial distribution 28
Multiple sequence alignment 111—118 193
Multiregional model 135
Multivariate function 186—187
Mutations 137 138
Mycoplasma genitalia 68
Needleman — Wunsch algorithm 107
Needleman — Wunsch edit distance 91—94
Neighbor relation 166
Neighborhood system 44
Net pairwise potential 225
Neutral networks 203 205
Neutral substitutions 139
Non-covalent bond 3
Normal distribution 30—31
Normalized specific amino acid distance frequency 225
NP-hardness 258
Nuclear magnetic resonance (NMR) studies 226
Nucleic acids 6—13
Nucleotide entropy 66—68
Nucleotide sequences 66 139—144
nucleotides 4—8
Nucleotides, forms 8
Nussinov — Jacobson matrix 208
Odds ratio 86
Oligonucleotides 6
Open reading frame (ORF) 2
Operational taxonomic unit (OTU) 137
ordering constraints 248
organic chemistry 3
Overlay matrices 100
Pair group method (PGM) 148
Pair probabilities, maximum-likelihood estimation 132—133
PAM matrices 86—88 139 140
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