Clote P., Backofen R. — Computational Molecular Biology :: Электронная библиотека попечительского совета мехмата МГУ

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Clote P., Backofen R. — Computational Molecular Biology

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Название: Computational Molecular Biology

Авторы: Clote P., Backofen R.

Аннотация:

Primarily aimed at advanced undergraduate and graduate students from bioinformatics, computer science, statistics, mathematics and the biological sciences, this text will also interest researchers from these fields.

Язык:

Рубрика: Биология/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 2000

Количество страниц: 287

Добавлена в каталог: 29.11.2005

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID

Предметный указатель

$\beta$ 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 $\beta$ 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 $\delta$ -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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