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Salzberg S., Searls D., Kasif S. — Computational methods in molecular biology
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Название: Computational methods in molecular biologyАвторы: Salzberg S., Searls D., Kasif S.Аннотация: Computational biology is a rapidly expanding field, and the number and variety of computational methods used for DNA and protein sequence analysis is growing every day. These algorithms are extremely valuable to biotechnology companies and to researchers and teachers in universities. This book explains the latest computer technology for analyzing DNA, RNA, and protein sequences. Clear and easy to follow, designed specifically for the non-computer scientist, it will help biologists make better choices on which algorithm to use. New techniques and demonstrations are elucidated, as are state-of-the-art problems, and more advanced material on the latest algorithms. The primary audience for this volume are molecular biologists working either in biotechnology companies or academic research environments, individual researchers and the institutions they work for, and students. Any biologist who relies on computers should want this book. A secondary audience will be computer scientists developing techniques with applications in biology. An excellent reference for leading techniques, it will also help introduce computer scientists to the biology problems. This is an outstanding work which will be ideal for the increasing number of scientists moving into computational biology.
Язык: Рубрика: Computer science /Статус предметного указателя: Готов указатель с номерами страниц ed2k: ed2k stats Год издания: 1998Количество страниц: 399Добавлена в каталог: 20.08.2014Операции: Положить на полку |
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160 161 3D motif 208 5'/3' compensation effect 160 Acceptor 110 113 Actin 292 ADE 357 Affine gap penalties 237 242 252 Alewife 34 Amino acid substitution matrices 213 219 222 Anfinsen, C. 4 Asilomar Competition 309 Aspartyl proteinases 289 Associative memory 325 ATP binding sites 214 215 217—219 b-trefoil folds 309 Baeck, T. 170 Baeck-propagation 113 115 Baum — Welch algorithm 349 Baumann, G. 290 Bayes' law 24 25 211 216 247 338 Bayes' networks 335 BCM Gene Finder 355 Benner, S. 237 Binary trees 256 bioWidgets 360 BLAST 6 7 14 15 33 35 76 90 92 93 97—99 120 121 357 BLASTP 136 BLASTX 75 76 Block Maker 34 BLOCKS 96 BLOSUM matrices 32 88 221 Booker, L. 183 Bowie, J. 291 292 Branch and bound 21 236 256 268 269 272 Branch point 143 Breathnach, R. 138 Breiman, L. 188 190 Brunak, S. 162 Bryant, S. 234 237 272 273 Building block hypothesis 168 173 Buntine, W. 191 Buried polar residues 292 300 Burks, C. 175 Burset, M. 199 C4.5 188 Calcium binding sites 214 CAP2 34 CART 188 Casari, G. 291 Case-based reasoning 65—85 CASP (Critical Assessment of techniques for protein Structure Prediction) 5 309 CATH 87 100 Causal trees 341 Censor 35 Chain graphs 337 Chain-chain docking 321 Chambon, P. 138 CHARMM 290 Chou — Fasman propensities 293 Chou, P. 293 Clark, P. 191 Classification 17 87 91 92 95 99 102 192 210 211 351 CLUSTALW 34 Clustering 91 94 95 320 Codon usage 7 30 58 CoG 96 Cohen, F. 290 COMPEL 70 Computational complexity 262—267 Computational efficiency 5 14 15 94 95 123 124 165 244 256 257 260 278 Computer assisted drug design 313 Computer vision 313 324 325 Conditional probability 24 57 112 113 212 247 336 337 342 Connolly, M. 314 319 Convergent evolution 92 Core template selection 236 239 248 Cramer, M. 171 Crippen, G. 237 291 Cross-validation 211 218 Crossover 304 Crossover (in genetic algorithms) 168—174 181 Data Mining 65 Dayhoff, M. 32 89 93 dbEST 91 120 358 DDBASE 100 DDBJ 66 Decision trees 18 19 157 187—202 Decision trees, pruning 190 def 100 Definite clause grammar (DCG) 71 Delcher, A. 342 Dinucleotide preferences 57 Discriminant analysis 162 Disulfide bonding cysteines 214 Dock 314 docking 313—332 Donor 110 113 Doolittle, R. 39 287 Dot plots 32 33 Double dynamic programming 305—308 DSSP 273 302 Dust 35 Dynamic programming 6 22 23 26 32 54 101 110 118 119 122 123 194—198 222 234 236 240 267 292 304 305 308 Dynamic programming, frame consistent 198 EcoParse 61 Eddy, S. 61 Ef Tu 292 Eisenberg, D. 290 292 EM algorithm 348—350 EMBL 33 66 143 Entrez 358 EpoDB 70—75 359 Evidence nodes 344 345 Evolutionary algorithms 165—184 Exons 30 37 60 79 81 109 121 126 188 197 Expectation maximization (EM) 349 Expressed sequence tags (ESTs) 36 110 120 121 126 127 FAKtory 34 360 Fasman, G. 293 FASTA 6 14 15 33 77 79 97 Fauchere, J. 293 Feature 208 Feller, W. 336 FGENEH 194 201 Fickett, J. 192 Finkelstein, A. 292 Fitness functions 166 172 176 Flavodoxin 292 Flexible docking 317 FLEXX 314 Floeckner, H. 237 Fogel, D. 171 Fogel, L. 171 Fold libraries 288 Fold recognition 231 287 Folding pathway 286 Forney, G. 346 Frame shifts 117 125 Fraser, C. 201 FSSP 100 222 GAP4 34 Gapped block alignment 232 236 237 gdb 359 GenBank 33 66 70 82 83 88 91 93 98 126 136 143 152 153 180 199 GeneID 194 355 GENEMARK 38 58 194 358 GeneParser 194 196 356 Genetic algorithms 167—174 183 303 304 genetic code 30 Genetic programming 171 Genie 61 194 196 200 356 GenLang 356 GenQuest 355 GenScan 61 68 84 130 136 194 196 200 201 355 Geometric hashing 314 324—331 Geometric pattern matching 315 332 Gibbs, A. 32 Gibrat, J.-F. 351 Gish, W. 92 Glimmer 38 194 201 357 Gotoh, O. 308 Grail 68 84 109—111 113—117 120—122 126 127 194 196 200 355 Grammar 56 71 72 76—78 80 84 Greedy algorithms 182 Greer, J. 236 Gregoret, L. 290 Guigo, R. 199 Haussler, D. 349 351 Heat-shock protein 292 Hemoglobins 231 Henderson, J. 162 Hendlich, M. 290 291 296 297 Henikoff, S. 32 Hexamer frequency 111 192 HHS 95 96 102 359 Hidden Markov models 5 23—25 34 37 45—62 91 96 102 133 134 162 196 200 339 343 344 349 351 HIV protease 289 HMMER 61 HMMgene 61 Holland, J. 168 Holm, L. 290 Homology modeling 5 6 229 HSSP 101 Hughey, R. 61 Human Genome Project (HGP) 29 65 91 Hydrogen bonding 286 Hydrophobic collapse 228 Hydrophobic core 300 Hydrophobic forces 230 Hydrophobic potential 291 Hydrophobicity 213 291 297 Hydrophobicity plot 39 ID3 188 Interest points 316—318 320 327 Intermolecular penetration 327 329 Interpolated Markov models (IMMs) 201 358 Introns 30 37 60 79 81 129 188 197 Inverse Boltzmann equation 293 295 Inverse folding 291 292 Inverse structure prediction 249 Jiang, F. 314 Jones, D. 236 Kabsch, W. 302 Karlin, S. 130 Karplus, M. 290 Katchalski-Katzir, E. 314 Kel, A. 70 Kel, O. 70 Kim, S. 314 Kinase domain 89 Kleffe, J. 162 Kolchanov, N. 70 Koza, J. 171 Kozak, M. 196 Krogh, A. 349 Kulp, D. 136 Kuntz, I. 314 319 Kyte, J. 39 Lactate dehydrogenase 294 Laterally transferred genes 40 Lattice representation 293 Lawrence, C. 234 237 272 273 Lemer, C. 237 Lengauer, T. 314 Lens 359 Levinthal paradox 286 Library of Protein Family Cores (LPFC) 222 223 Log-odds score 48 49 54 Long-range interactions (in splice sites) 147—155 LPFC 101 Luethy, R. 290 292 MACAW 34 Machine learning 211 335 342 Maiorov, V. 237 291 Mann — Whitney Rank-sum test 209 MAP 34 MarFinder 356 Markov assumption 337 Markov chains 24—26 31 36—38 109 111 112 135 146 187 193—196 201 202 339 344 Markov processes 342 Markov random fields (MRF) 233 248 Marr, T. 134 Maximal dependence decomposition (MDD) 157—162 196 202 McIntyre, G. 32 McLachlan, A. 30 290 Mean force potentials 297 Meme 34 Memory-based reasoning 17 Minimum spanning tree 94 Morgan 194—198 355 Motif 46—50 89 91 92 94 98 162 215 216 233 236 237 242 250 257 278 Moult, J. 309 Mount, S. 138 196 Mouse 81 82 MS-DOT 316 MSA (multiple sequence alignment) 6 7 33 34 47 50 55 61 90 96—98 101 223 289 291 Murthy, S. 188 189 Myers, E. 34 MZEF 356 NCBI 358 Needleman, S. 295 NetPlantGene 356 Neural networks 19 109—127 Neyman — Pearson lemma 133 Niblett, T. 192 Non-deterministic polynomial time 264 Novotny, J. 289 290 NP-complete 15 16 95 165 263—266 NP-completeness of threading 265—267 NP-hard 235 236 263 265 343 Nuclear magnetic resonance (NMR) 207 OC1 188 Optimization 166 Orengo, C. 305 308 Orthologous genes 75 81 Ouzounis, C. 279 Overfitting 211 Pairwise alignment 31—33 45 54 87 165 222 229 289 Pairwise homology, sequence similarity 92 Pairwise potentials 290—293 PAM matrices 14 32 88 Paralogous genes 75 PAUP 34 PDB 207 218 219 321 330 PDD 359 Pearl, J. 343 346 Permutation Problems 176 178 Pfam 95 96 102 PHYLIP 34 Pileup 34 Pima 34 97 PIR 97 Pliska, V 293 PolyA sites 79 Ponder, J. 291 Position asymmetry 193 Position weight matrix (PWM) 195 Pre-mRNA splicing 130—132 Principle of optimality 22 prints 98
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