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Salzberg S., Searls D., Kasif S. — Computational methods in molecular biology
Salzberg S., Searls D., Kasif S. — Computational methods in molecular biology

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Название: Computational methods in molecular biology

Авторы: 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: en

Рубрика: Computer science/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 1998

Количество страниц: 399

Добавлена в каталог: 20.08.2014

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID
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Предметный указатель
$G_{3}$ preference effect      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 $\zeta$-globin gene      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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