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Koonin E.V., Galperin M.Y. Ч Sequence - Evolution - Function: Computational Approaches in Comparative Genomics
Koonin E.V., Galperin M.Y. Ч Sequence - Evolution - Function: Computational Approaches in Comparative Genomics

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Ќазвание: Sequence - Evolution - Function: Computational Approaches in Comparative Genomics

јвторы: Koonin E.V., Galperin M.Y.

јннотаци€:

Designed as an introduction to the field of computational methods for comparative and functional genomics, this text explains the computer methods from the user's viewpoint, without the details of the math and algorithms. The history of the field, various genome sequencing projects, the conceptual basis of the field, evolutionary principles of protein function assignments, and databases of genomic data are the book's main topics. Both authors are affiliated with the National Institutes of Health in Bethesda, Maryland.


язык: en

–убрика: Ѕиологи€/

—татус предметного указател€: √отов указатель с номерами страниц

ed2k: ed2k stats

√од издани€: 2003

 оличество страниц: 463

ƒобавлена в каталог: 18.03.2007

ќперации: ѕоложить на полку | —копировать ссылку дл€ форума | —копировать ID
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ѕредметный указатель
AAindex      103 130
AAT      114 125
Aeropyrim pernix      208Ч211 307
Aeropyrim pernix, annotation      208Ч211
Aeropyrim pernix, aro genes      223
Aeropyrim pernix, number of protein folds      364
Aeropyrim pernix, phosphofructokinase      303
Aeropyrim pernix, TCA cycle      315
Agrobacterium tumefaciens annotation      197
Agrobacterium tumefaciens annotation, orimithine cyclodeaminase      344
Algorithm, BLAST      134Ч136 146Ч147 156Ч158
Algorithm, FASTA      146 162
Algorithm, Needleman Ч Wunsch      10 141
Algorithm, Smith Waterman      11 119 141 144Ч146 162 223
Aminoacyl-tRNA symthetases      46 237Ч239 257 267Ч270
Aminoacyl-tRNA symthetases, asparaginyl      46
Aminoacyl-tRNA symthetases, glycyl      45 46
Aminoacyl-tRNA symthetases, glytaminyl      46 237Ч238
Aminoacyl-tRNA symthetases, lysyl      215 357
Aminoacyl-tRNA symthetases, tryptophanyl      238Ч239
Anabaena sp.      197 286Ч292
Ankyrin      65Ч67 71
Antibiotics      44 58 295 353Ч357
Apoptosis      281Ч294
Aquifex aeolicus      41 43 48 235 259 306 309 330 364
Arabidopsis thaliana      62 161 169 176 279 369Ч370
Arabidopsis thaliana, databases      88 93Ч94
Arabidopsis thaliana, gene prediction      122Ч124
Archaeoglobus fulgidus      63 276 303 306 311 324Ч330 337
Archaeoglobus fulgidus, gene expansion      24Ч25
ATP-grasp      68 78 171 318 320 324Ч326
ATPase, P-loop      8 9 64 148Ч149 205 213 267Ч270 285
ATPase, PP-loop      10 329 378
Bacillus subtilis      41 44 46 49 74 91 112 217 291 309Ч315 330 338 341 350 364
bind      100Ч101
BLAST      11 81Ч82 114 134Ч136 139 146Ч147 156Ч172
BLAST, parameters      160Ч164
BLAST, unfinished genomes      81Ч82
BLOCKS      55 68Ч69 73 86 129
Breast cancer protein      160 172
Breast cancer protein, BRENDA      102
Breast cancer protein, BRITE      99Ч100
Buchnera sp.      38 323 330 342
Caenorhabditis elegans      41 86 94Ч95 122Ч124 199 225 275
Caenorhabditis elegans, databases      94Ч95
Caspase      151 153 276 282Ч294
CATH      33 76Ч80 190 362 365
CD search      74 167Ч174
CDD      6 9 63 70Ч74
Chlamydia      37 40 82 214 241 251 276 303 309 323 334Ч339 357Ч358
ChloroP      184
Clustal      145 192
CMR      87Ч88
COG database      23 39 47Ч49 72 83Ч84 195 200 205Ч222
Coiled coil      168Ч169 184 196
DALI      32Ч33 76 190
DAS      183 186
Databases, archival      54 57 207
Databases, curated      53 55Ч61 69Ч74 77Ч86 101 210
Databases, domain      69Ч74
Databases, motif      64Ч69 73
Databases, sequence      51Ч57
databases, structure      75Ч80
Deinococcus radiodurans      48 56 58 241 310 351 364
DIP      100
Domain      6Ч9 28Ч34 41 64 69Ч77 86 140 148Ч164 167Ч176 185 198 206Ч207 216 219 287Ч296 367Ч374
Domain of life      230Ч234 246Ч248 369
Domain, "promiscuous"      64 219 329 374
Domain, databases      69Ч74
Domain, fusions      216Ч219
Domain, signaling      41 217 281 372
Drosophila melanogaster      88 95Ч97 100 120Ч124 137Ч138
Drosophila melanogaster, databases      95Ч96
DSC      186 188
Edgar Allan Poe      141Ч144
Encephalitozoon cuniculi      115
enzyme      55 102Ч103
EPD      101
ERGO      85 200Ч221 225
Errors in annotation      57Ч63 199Ч205
Escherichia coli, databases      89Ч90
FFAS      190Ч191
fold      33Ч34 75Ч77 189Ч192 268 272 363Ч375
Fold in complite genomes      366
Fold, classification      76Ч77
Fold, most common      369
Fold, recognition      189Ч192
Fold, Rossmann      34 257 266 291 366Ч369
Fold, TIM-barrel      33 77 366 369
FSSP      32Ч33 76 80
FUGUE      190 192
GenBank      11 51Ч56 75 81Ч82 98 104 162Ч163
GenBank, annotations      58Ч59 63 195 202Ч207
Gene, acquisition      42 239Ч240 247 274Ч279 285Ч294 371
Gene, duplication      35Ч37 40 44
Gene, loss      36Ч40 43 47 178 213Ч214 229Ч230 235Ч248 295 324 359 385
Gene, order      12 35 37 220Ч226 236 248Ч249 264
GeneBuilder      122
GeneFinder      123
GeneID      123
GENEMARK      122
GeneParser      123
Genes and Disease      96
GeneSplicer      124
GeneWise      125
Genie      122
GenScan      121Ч122
GenThreader      190Ч191
Glimmer      120 122
Gold      14 19
GOR      187
Grail      120Ч122
Haemophilus influenzae      13 37Ч40 46 81 87 217 220 309 319Ч323 339 356Ч357
Haemophilus influenzae, Halobactetium      222 252 301 303 305 337
Helicobacter pylori      40 41 63 215 217 303 306 311 316 328Ч329 341Ч342 356Ч357
Hidden Markov models      11 69Ч71 87Ч88 121Ч123 156Ч157 173 183Ч187 191Ч193
HMMgene      123
HMMTop      183
HNN      188
Holliday junction DNA resolvase      46 175
Homo sapiens, datobases      96Ч97
Homo sapiens, genes      160Ч161 166Ч171 238
HomoloGene      97
Horizontal gene transfer      42Ч44 208 221 230Ч252 264Ч265 274Ч278 291Ч296 311 344 358 369 379 383 384
HSPL      124
Iduronate sulfatase      115Ч117
InBGU      190Ч191
InterPro      55 69Ч73
Jnet      185
Jped      184Ч186
Karlin Ч Altschul statistics      134Ч136 141 165 386
KEGG      84Ч85 91 102Ч103 196 207 224Ч225 300
KLOTHO      102
Lactococcus lactis      197 322 341
Lateral gene transfer      see Horizontal gene transfer
Ligand      103
Listeria      197 335
LocusLink      81 96Ч97 101
LOOPP      192
Low complexity      71 136Ч139 160Ч161 167Ч174 204Ч206
Lysozyme      28 30Ч33 126
MACAW      151 154
Mastermind      137Ч138
Matrix      see Substitution matrix
MBGS      85
Memsat      183
Mitoprot      184
MLRC      188
MMDB      31 54 76Ч77 104
Motif      see Sequence motif
Multicoil      185Ч186
MUMmer      87
Mycobacterium      38 40Ч41 195 318 326 353
Mycoplasma      37Ч40 45Ч47 198Ч201 319 353
MZEF      123
NetGene      124
NNSplice      124
NNSSP      186Ч187
Non-orthologous gene displacement      43Ч48 213Ч214 238 258Ч260 299Ч356
OMIM      23 54 88 96 115 116 160 404
ORF finder      84 112Ч114
ORFGene      125
Orpheus      114
P-loop NTPases      267Ч270 285 363Ч368
Parcoil      185
PDB      30Ч32 75Ч78 153 159 190Ч191 199 363
PEDANT      86 88 114 200
Pfam      9 55 69Ч74 86 88 90 121 157 173 176 196 198
PHD      183Ч187 200Ч201
Phosphoglycerate mutase      46 48Ч49 59 62 78 214 305
Phosphomopyruvate decarboxylase      58Ч59 63
Phyletic patterns (profiles)      39 47Ч49 176 208 212Ч219 235Ч236 240Ч244 255Ч259 281 285 300Ч358 376Ч379
Phyletic patterns (profiles), complementare      48Ч49 214Ч215
Phyletic patterns (profiles), identical      217
Phyletic patterns (profiles), use in annotation      207Ч210 212Ч219
PipMaker      125
PIR      53Ч63 86 92 106 109 208
Polyketide symthase      45 62 112
Power law      370Ч374 385
PREDATOR      186Ч187
PredictProtein      186
Predotar      184
prints      69 73
Procrustes      125
ProDom      55 69 72Ч73
prof      186 188
PROSITE      55 64Ч73 86 87 90 148Ч150 200 355
Protease      79 151Ч155 162 276Ч277 282Ч284
Protein mutant database      103
PSA      187
Pseudogene      22 53 118 197
Pseudogene, PHI-BLAST      158 177 180
Pseudogene, PSI-BLAST      34 156Ч158 165Ч173
Pseudogene, PSIpred      186Ч187
Pseudogene, PSORT      182Ч184
Pseudogene, PSSP      186 188
Ribonuclease HII      46
Ribosomal, database project      98Ч99
Ribosomal, proteins      26Ч27 112Ч113 134 148 258 355
Ribosomal, RNA      18 38 98Ч99 230 246Ч252 257 355
Rickettsia      48 215 300 327 351 358 366
RMSD      76
RNA polymerase, RPFOLD      192
RNA World      299 254 266Ч272
RPS-BLAST      74 157Ч158
Saccharomyces cerevisiae      see Yeast
SAM-T99      186Ч187 190Ч191
scop      9 11 33 77 80 86 190 192 361 365Ч366
SEG      137Ч139 160Ч161 201 see
Sepatation anxiety      62
Sequence, identity      30 34 76 126 142 148 158 162 196 402
Sequence, logo      67
Sequence, motif      11Ч12 28 55 64Ч69 72 77Ч78 148Ч156 172 175Ч179 201 205 275 285 301 341 362
SignalIP      182
Sinorhizobium meliloti      197
SMART      9 41 71Ч74 157 173 189 196 198 207
SOSUI      183Ч184
Splice site prediction      124
SpliceView      124
SSPro      186 188
Structure databases      see CATH MMDB PDB SCOP
Substitution matrix, BLOSUM      68 129Ч132 143 154Ч156 162Ч163
Substitution matrix, PAM      129Ч131 154Ч155 163
SUPERFAMILY      190 192
Swiss-Prot      53Ч64 69Ч73 102
Synechocystic sp      40Ч41 71 91 279 351 366
TargetP      184
Thermoanaerobacter tengcongensis archael genes      236
Thymidylate synthase      59 215
TMAP      183Ч184
TMHMM      183Ч184 186
TMpred      183
TopPred      183 186
TRANSFAC      99
Treponema pallidum      99 217 242 251 299 306 307 309 319 356Ч357
UCLA/DOE Fold Server      191
VAST      32Ч33 76 190
Vibrio cholerae      134 148 358
WIT      85 196 200 207 210 221 225 300
Xylella fastidiose      304 309
Yeast      11 23 24 38Ч41 67 86 92Ч93 99Ч100 114 122Ч124 214
Yeast, databases      92Ч93 99Ч100
Yeast, genome      11 114
Yersinia pestis      62 89 197 209
Zpred      186 188
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