Series Preface |
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xi | |
Preface |
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xiii | |
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1 | (22) |
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3 | (1) |
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4 | (2) |
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6 | (1) |
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6 | (8) |
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6 | (2) |
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8 | (5) |
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13 | (1) |
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14 | (3) |
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14 | (1) |
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15 | (2) |
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17 | (4) |
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17 | (2) |
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Transcription and Translation |
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19 | (2) |
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21 | (2) |
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Acknowledgements and References |
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22 | (1) |
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23 | (58) |
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23 | (30) |
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25 | (2) |
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Some Important Probability Distributions |
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27 | (11) |
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38 | (5) |
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Metropolis-Hastings Algorithm |
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43 | (4) |
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Markov Random Fields and Gibbs Sampler |
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47 | (5) |
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52 | (1) |
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Combinatorial Optimization |
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53 | (8) |
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53 | (1) |
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54 | (1) |
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Heuristics Related to Simulated Annealing |
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54 | (1) |
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Applications of Monte Carlo |
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55 | (5) |
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60 | (1) |
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Entropy and Applications to Molecular Biology |
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61 | (11) |
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Information Theoretic Entropy |
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62 | (1) |
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Shannon Implies Boltzmann |
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63 | (3) |
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Simple Statistical Genomic Analysis |
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66 | (3) |
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Genomic Segmentation Algorithm |
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69 | (3) |
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72 | (5) |
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Appendix: Modification of Bezout's Lemma |
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77 | (4) |
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Acknowledgements and References |
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79 | (2) |
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81 | (54) |
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83 | (1) |
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84 | (4) |
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Global Pairwise Sequence Alignment |
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88 | (23) |
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88 | (11) |
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Alignment with Tandem Duplication |
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99 | (11) |
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110 | (1) |
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Multiple Sequence Alignment |
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111 | (7) |
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112 | (1) |
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112 | (2) |
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114 | (3) |
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117 | (1) |
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117 | (1) |
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118 | (2) |
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Locating Cryptogenes and Guide RNA |
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120 | (3) |
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Anchor and Periodicity Rules |
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122 | (1) |
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122 | (1) |
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Expected Length of gRNA in Trypanosomes |
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123 | (5) |
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128 | (4) |
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Appendix: Maximum-Likelihood Estimation for Pair Probabilities |
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132 | (3) |
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Acknowledgements and References |
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133 | (2) |
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135 | (40) |
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135 | (2) |
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Rate of Evolutionary Change |
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137 | (7) |
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137 | (2) |
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139 | (5) |
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144 | (13) |
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147 | (5) |
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152 | (4) |
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Estimating Branch Lengths |
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156 | (1) |
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157 | (9) |
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159 | (1) |
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Recursive Definition for the Likelihood |
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160 | (2) |
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Optimal Branch Lengths for Fixed Topology |
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162 | (4) |
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166 | (1) |
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166 | (5) |
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169 | (1) |
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170 | (1) |
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171 | (4) |
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Acknowledgements and References |
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173 | (2) |
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175 | (26) |
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Likelihood and Scoring a Model |
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177 | (3) |
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Re-estimation of Parameters |
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180 | (13) |
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181 | (3) |
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EM and Justification of the Baum-Welch Method |
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184 | (3) |
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Baldi--Chauvin Gradient Descent |
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187 | (4) |
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191 | (2) |
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193 | (4) |
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Multiple Sequence Alignment |
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193 | (1) |
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194 | (1) |
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Eukaryotic DNA Promotor Regions |
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195 | (2) |
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197 | (4) |
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Acknowledgements and References |
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198 | (3) |
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201 | (62) |
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202 | (11) |
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213 | (10) |
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Amino Acid Pair Potentials |
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223 | (5) |
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Lattice Models of Proteins |
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228 | (6) |
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Monte Carlo and the Heteropolymer Protein Model |
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231 | (2) |
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Genetic Algorithm for Folding in the HP Model |
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233 | (1) |
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Hart and Istrial's Approximation Algorithm |
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234 | (9) |
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234 | (2) |
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236 | (3) |
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Block Structure, Folding Point, and Balanced Cut |
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239 | (4) |
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Constraint-Based Structure Prediction |
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243 | (3) |
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246 | (13) |
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246 | (3) |
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A Branch-and-Bound Algorithm |
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249 | (9) |
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258 | (1) |
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259 | (4) |
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Acknowledgements and References |
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261 | (2) |
Appendix A Mathematical Background |
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263 | (2) |
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A.1 Asymptotic complexity |
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263 | (1) |
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263 | (1) |
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264 | (1) |
Appendix B Resources |
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265 | (4) |
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265 | (1) |
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266 | (3) |
References |
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269 | (12) |
Index |
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281 | |