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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.
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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
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Предметный указатель
Prior probability 24
Probabilistic models 133—135
Probabilistic networks 335—351
Probe 97
ProClass 97
Procrustes 357
ProDom 98
Profile hidden Markov models 49—55
PROF_PAT 98
Promoters 16 31 61 68 83
PROSITE 95 98
Protein domains 88 89 93 230 272
Protein protein docking 319—324
Protein structure prediction 4 5
Protein threading 16 17 221—224 227—280 285—310
Pruning decision trees 190
Pseudo-energies 235
Pseudocounts 50—54
Pyrimidine tract (in acceptor sites) 138 145 151
Quad-trees 256
Quinlan, J.R. 188 191
RAM 13
Rank-sum test 210
Rarey, M. 314
Receptor-ligand recognition see "Docking"
Reese, M. 136 162
Regular expressions 46 47
REPBASE 99
Repeat Pattern Toolkit 357
RepeatMasker 35
Repetitive sequence elements 87 90
Reva, B. 292
Ribosome binding site 31
Richards, F. 291
Richardson, Jane 230
Rigid docking 315 317 323 332
RNA lariat 132
Rooman, M. 286
Rossmann fold 216 295
Rotamer library 224
RPT 99
Salzberg, S. 190
SAM 34 61
Sander, C. 290 302
Satisfiability 265
SBASE 99
Schema theorem 168 173
scop 87 101
Scoring schemes (for threading) 278 279
SCWRL 224
Search space 4 19 20 87 166 167 228 256 257 259—262 268 303
Searls, D. 56 76
Secondary structure 38 67 234
Secondary structure prediction 251 254 344
SEG 35 93
Senapathy, P. 196
SENSEI 92
Sequence alignment see "Pairwise alignment"
Sequence analysis programs, ADE 357
Sequence analysis programs, BCM Gene Finder 355
Sequence analysis programs, GenelD 355
Sequence analysis programs, GeneMark 358
Sequence analysis programs, GeneParser 356
Sequence analysis programs, Genie 356
Sequence analysis programs, GenLang 356
Sequence analysis programs, GENSCAN 355
Sequence analysis programs, Glimmer 357
Sequence analysis programs, GRAIL 355
Sequence analysis programs, MarFinder 356
Sequence analysis programs, MORGAN 355
Sequence analysis programs, MZEF 356
Sequence analysis programs, NetPlantGene 356
Sequence analysis programs, PROCRUSTES 357
Sequence analysis programs, Repeat Pattern Toolkit 357
Sequence analysis programs, SorFind 357
Sequence analysis programs, SplicePredictor 357
Sequence analysis programs, TESS 358
Sequence analysis programs, THREADER 356
Sequence analysis programs, THREADER2 356
Sequence analysis programs, TIGR Assembler 358
Sequence analysis programs, VEIL 355
Sequence analysis programs, WebGene 358
Sequence annotation 89—91
Sequence signals 36
Sequence similarity see "Pairwise homology"
Sequence-structure alignment 227—280
Serine protease active sites 214
Shape complementarity 314
Shortest path 347
Side-chain interactions 279
Simulated annealing 303 304
Sippl, M. 234 290 291 295—297 300
Sirajuddin, K. 162
Small nuclear RNAs (snRNAs) 130
Smith-Waterman algorithm 15 33
Sodium binding sites 214
Solovyev, V 162
Solvation effects 295
Solvation energy model 290
Solvation potential 301
Solvent accessibility 234 292
SorFind 194 357
Speech recognition 45
Splice junctions 113 114
Splice sites 26 36 57 88 113 115 129—163 195 197 201
Spliceosome 129 131 143
SplicePredictor 357
Splitting rules 189 190
SSP (sequence structure parser) 71—73
Staden, R. 30 134
Starkweather, T. 178
Statistical entropy 297
Steric clashes 224
Stultz, C. 248
Super-secondary structures 250 257
Swapping 13
SwissProt 33 70 96—98 101 102
Taylor, W. 305 308
Tentative human consensus (THC) 36
Tertiary structure 39
TESS (Transcription Element Search Software) 69 83 358
THREADER 310 356
THREADER2 356
TIGR (The Institute for Genomic Research) 36 357
TIGR Assembler 35 358
TIM (Triose phosphate isomerase) 294
TIM barrels 295 309
Torsion angles 285
Torsion space 285
Transcription elements 68 69 80
Transcription factors 68 80
TRANSFAC 70 80 83 359
TransTerm 359
Traveling salesman problem 15 175
TRRD 70
Tung, C.-S. 192
van der Waals effects 286 291 313 315 316
Variable loop regions 234 240 302
Variable-length gaps 235
VEIL 61 134 194 196 200 355
Virtual memory 13
Viterbi algorithm 23 54 59 343 346—349
WebGene 358
Weight array model (WAM) 134
Weight matrix models (WMMs) 134 136—147
White, J.V 248
Whitley, D. 183
Wilcoxon rank test 210
Windowed weight array model (WWAM) 145—147
Wu, T. 196
WU2BLAST 92
Wunsch, C. 295
X-ray crystallography 207
XNU 35 93
Yoo, N. 183
Zhang, M. 134
Zhang, X. 351
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