دانلود کتاب Problems and Solutions in Biological Sequence Analysis

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Cover......Page 1
Half-title......Page 3
Title......Page 5
Copyright......Page 6
Dedication......Page 7
Contents......Page 9
Preface......Page 13
1 Introduction......Page 17
1.1 Original problems......Page 18
1.2 Additional problems......Page 21
1.3 Further reading......Page 39
2.1 Original problems......Page 40
2.2 Additional problems and theory......Page 59
2.2.1 Derivation of the amino acid substitution matrices (PAM series)......Page 62
2.2.2.1 Theoretical introduction to Problems 2.19 and 2.20.......Page 73
2.2.3 Distribution of the length of the longest common word among several unrelated sequences......Page 78
2.3 Further reading......Page 81
3 Markov chains and hidden Markov models......Page 83
3.1 Original problems......Page 84
3.2 Additional problems and theory......Page 93
Theoretical introduction to Problems 3.20 and 3.21......Page 102
Theoretical introduction to Problem 3.23......Page 111
3.3 Further reading......Page 118
4 Pairwise alignment using HMMs......Page 120
4.1 Original problems......Page 121
4.2 Additional problems......Page 129
4.3 Further reading......Page 141
5 Profile HMMs for sequence families......Page 142
5.1 Original problems......Page 143
5.2 Additional problems and theory......Page 153
5.2.1 Discrimination function and maximum discrimination weights......Page 166
5.3 Further reading......Page 177
6 Multiple sequence alignment methods......Page 178
6.2 Additional problems and theory......Page 179
Theoretical introduction to Problem 6.2......Page 180
Theoretical introduction to Problem 6.3......Page 187
6.2.3 Gibbs sampling algorithm for local multiple alignment......Page 195
6.3 Further reading......Page 197
7.1 Original problems......Page 199
7.2 Additional problems......Page 227
7.3 Further reading......Page 231
8 Probabilistic approaches to phylogeny......Page 234
8.1 Original problems......Page 235
8.1.1 Bayesian approach to finding the optimal tree and the Mau--Newton--Larget algorithm......Page 251
8.2 Additional problems and theory......Page 275
8.2.1 Relationship between sequence evolution models described by the Markov and the Poisson processes......Page 280
Theoretical introduction to Problem 8.20......Page 286
8.2.3 More on the rates of substitution......Page 291
8.3 Further reading......Page 293
9 Transformational grammars......Page 295
9.1 Original problems......Page 296
9.2 Further reading......Page 306
10 RNA structure analysis......Page 307
10.1 Original problems......Page 308
10.2 Further reading......Page 324
11.1 Original problems......Page 327
11.2 Additional problem......Page 342
11.3 Further reading......Page 343
References......Page 344
Index......Page 359