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Percus J.K. — Mathematics of genome analysis
Percus J.K. — Mathematics of genome analysis

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Название: Mathematics of genome analysis

Автор: Percus J.K.

Аннотация:

The massive research effort known as the Human Genome Project is an attempt to record the sequence of the three trillion nucleotides that make up the human genome and to identify individual genes within this sequence. The description and classification of sequences is heavily dependent on mathematical and statistical models. This short textbook presents a brief description of several ways in which mathematics and statistics are being used in genome analysis and sequencing.


Язык: en

Рубрика: Computer science/Биоинформатика/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 2004

Количество страниц: 139

Добавлена в каталог: 20.11.2005

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID
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Предметный указатель
Allele      24
anchoring      18—23
Back propagation      115
Baker — Campbell — Hausdorf expansion      120
Base      2—3
Base, frequencies      42
Bayes' theorem      111
Benferroni inequality      83
Boltzmann equation      119
Chen — Stein theorem      86
Chi square test      44
Chromosome walking      16
Clone, density      18 22
Clone, end-characterized      36
Clone, library      9—12
Clone, resolved negative      31
Codon      6
Codon, dicodon usage      109
Concensus      108
Conjugate gradient method      114
Contig      13 14 40
Correlation coefficient      62
Correlation persistence      55
Correlation power law      67
Correlation ratio      43
Correlation window      61—64
Correlation, cross      55
Correlation, displaced      53
Correlation, factorial moments      64
Covariance and variance      54 61—65
Coverage      9 13 19
Cumulant expansion      17
Design, experimental      29
Diffusion      72
DNA      1—6
DNA, complementary      62
DNA, dynamics      123—126
DNA, functional regions      42
DNA, inhomogeneity in      73 126
DNA, strand symmetry      54
DNA, supercoiled      118
DNA, thermal behavior      118—123
Dot matrix      50 102
Dynamical programming      102
entropy      see also "Information"
Entropy per site      79
Entropy, Jensen — Shannon      49
Equivalent linearization      124
evaporation      123
Evolution, stochastic      57
Exon      4 60 108—111
Expansion-mutation model      56—57
Fingerprint assembly      13—18 36—41
Fokker — Planck equation      72
Form factor, for repeated pattern      74
Fragment size distribution      7
Gel electrophoresis      7
Gene      3 4 24 27
Generating function      24 38 51 59
Hidden layer      113
Hopfield network      115
Hurst index      67
Incidence matrix      30
Inclusion-exclusion theorem      32
Indel      96 99—100
information      see also "Entropy"
Information, content      104—105
Information, mutual      56
Information, power spectrum      73—78
Intron      4 108—111
Island      13 18 36
Isochore      49 66 69
JWKB method      122
kurtosis      65
Lagrangian form      124—125
Likelihood      47 105
Linkage unit, genetic      23
Map, linkage      23
Map, physical      13
Map, restriction      10
Markov models, basic      8
Markov models, hidden      67—69
Markov models, higher order      47
Markov models, walking      69—73
Matching      81
Matching, aligned      92 102
Matching, asymptotic expansion      87—89
Matching, common pattern      103
Matching, gaps      99
Matching, greedy      93
Matching, imperfections      92
Matching, indels      96 102
Matching, independence model      85
Matching, mismatch      94
Matching, mutual exclusion model      82
Matching, N-tuplet      103
Matching, penalty-free      97
Morse potential      123
Neural network      113
Ocean      13
Orthogonal patterns      117
Partial digestion      10
Partition function      119
Patch model      65—67
Penrose discriminant      110
Perceptron      113
Persistence length      118
pooling      28—35
Power spectrum      73—78
Probability distribution, chi square      46
Probability distribution, cluster size      61
Probability distribution, extreme value      89
Probability distribution, Gumbel      90 93
Probability distribution, normal      91
Probability distribution, Poisson      17 85 93
Protein      5 8 92 104
Purine      3 55
Pyrimidine      2 55
Random incidence      34
Reading frame      6
Reading frame, open      61
Repeats, exon      60
Repeats, longest      49
Repeats, simple sequence      58
Repeats, subsequence      78
Repeats, tandem variation      27
Restriction enzyme      6 10
Restriction fragment length polymorphism      23
RNA      5
RNA, splice signal      108
Runs, distribution of      81—91
Score      see also "Sequence comparision"
Score, acquisition      100—103
Score, distribution      92
Score, linear regime      100—101
Score, log regime      94 101
Score, non parametric      96
Score, phase transition      96
Score, phase trasition      96
Sequence comparison      see also "Matching"
Sequence comparison, dissimilarity      101
Sequence comparison, scrambled      56
Sequence comparison, shuffled      65
Sequence-tagged site      18
Sequencing methods, anchoring      18
Sequencing methods, fingerprint      13
Sequencing methods, hybridization      23
Sequencing methods, optical      10
Sequencing methods, shotgun      36
Sigmoidal form      112
Statistical models of sequence correlation, cluster distribution      61
Statistical models of sequence correlation, expansion-mutation      56—57
Statistical models of sequence correlation, hidden Markov      67—69
Statistical models of sequence correlation, patch model      65—67
Statistical models of sequence correlation, walking Markov      69—73
Stirling approximation      25 45 91 105
Subsequence analysis, categories      108
Subsequence analysis, clusters      109
Subsequence analysis, linear disriminant      109
Subsequence analysis, repeats      78
Training set      114
Transcription      5
Transcription, bubble      118
Transform, Fourier      24 74
Transform, Laplace      24
Transform, Walsh      76
Transform, wavelet      77
Transition operator      120
Translation      5
van Hove theorem      120
Vector      10
Venn diagram      83
Weight matrix      103
Window, correlation between      64
Window, correlation within      61—63
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