图书介绍
BIOLOGICAL SEQUENCE ANALYSISPDF|Epub|txt|kindle电子书版本网盘下载
- R.DURBIN 著
- 出版社： 清华大学出版社
- ISBN：
- 出版时间：2002
- 标注页数：356页
- 文件大小：116MB
- 文件页数：367页
- 主题词：
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图书目录
1 Introduction1
1.1 Sequence similarity, homology, and alignment2
1.2 Overview of the book2
1.3 Probabilities and probabilistic models4
1.4 Further reading10
2 Pairwise alignment12
2.1 Introduction12
2.2 The scoring model13
2.3 Alignment algorithms17
2.4 Dynamic programming with more complex models28
2.5 Heuristic alignment algorithms32
2.6 Linear space alignments34
2.7 Significance of scores36
2.8 Deriving score parameters from alignment data41
2.9 Further reading45
3 Markov chains and hidden Markov models46
3.1 Markov chains48
3.2 Hidden Markov models51
3.3 Parameter estimation for HMMs62
3.4 HMM model structure68
3.5 More complex Markov chains72
3.6 Numerical stability of HMM algorithms77
3.7 Further reading79
4 Pairwise alignment using HMMs80
4.1 Pair HMMs81
4.2 The full probability of x and y, summing over all paths87
4.3 Suboptimal alignment89
4.4 The posterior probability that xi is aligned to yj91
4.5 Pair HMMs versus FSAs for searching95
4.6 Further reading98
5 Profile HMMs for sequence families100
5.1 Ungapped score matrices102
5.2 Adding insert and delete states to obtain profile HMMs102
5.3 Deriving profile HMMs from multiple alignments105
5.4 Searching with profile HMMs108
5.5 Profile HMM variants for non-global alignments113
5.6 More on estimation of probabilities115
5.7 Optimal model construction122
5.8 Weighting training sequences124
5.9 Further reading132
6 Multiple sequence alignment methods134
6.1 What a multiple alignment means135
6.2 Scoring a multiple alignment137
6.3 Multidimensional dynamic programming141
6.4 Progressive alignment methods143
6.5 Multiple alignment by profile HMM training149
6.6 Further reading159
7 Building phylogenetic trees160
7.1 The tree of life160
7.2 Background on trees161
7.3 Making a tree from pairwise distances165
7.4 Parsimony173
7.5 Assessing the trees: the bootstrap179
7.6 Simultaneous alignment and phylogeny180
7.7 Further reading188
7.8 Appendix: proof of neighbour-joining theorem190
8 Probabilistic approaches to phylogeny192
8.1 Introduction192
8.2 Probabilistic models of evolution193
8.3 Calculating the likelihood for ungapped alignments197
8.4 Using the likelihood for inference205
8.5 Towards more realistic evolutionary models215
8.6 Comparison of probabilistic and non-probabilistic methods224
8.7 Further reading231
9 Transformational grammars233
9.1 Transformational grammars234
9.2 Regular grammars237
9.3 Context-free grammars242
9.4 Context-sensitive grammars247
9.5 Stochastic grammars250
9.6 Stochastic context-free grammars for sequence modelling252
9.7 Further reading259
10 RNA structure analysis260
10.1 RNA261
10.2 RNA secondary structure prediction267
10.3 Covariance models: SCFG-based RNA profiles277
10.4 Further reading297
11 Background on probability299
11.1 Probability distributions299
11.2 Entropy305
11.3 Inference311
11.4 Sampling314
11.5 Estimation of probabilities from counts319
11.6 The EM algorithm323
Bibliography326
Author index345
Subject index350