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| Ïîèñê ïî óêàçàòåëÿì |
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| Brown S.M. — Bioinformatics: A Biologist's Guide to Biocomputing and the Internet |
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| Ïðåäìåòíûé óêàçàòåëü |
ABI automated sequencers 135
Actinobacillus actinomycetemo-comitans 14
Algorithms 58
ALLALL 95
Anfinsen's dogma 105
ANGIS 42
ANTHERPROT 108
Applied Biosystems 135
Archaebacteria 17—18
Assembler 144
Australian National Genomic Information Service (ANGIS) 42
Automated DNA sequencing 11
Automated sequencers 135
Autoradiograms 134—135 135f
B. subtilis genome sequencing project 23—24
Baran, Paul 31
Basic Local Alignment Search Tool (BLAST) 14 37—38 58—60 64 72—78 74f 101
Basic Local Alignment Search Tool (BLAST) vs. FASTA 77—78
BCM GeneFinder 102
BCM Search Launcher 9 88 110
Berners — Lee, Tim 32
BESTFIT 87
Bioinformatics, change 4
Bioinformatics, defined 3
Bioinformatics, genome 19—20
Bioinformatics, trends 3—4
Biology Workbench 6
Biomolecular Research, Tools Pedro's 7
BioNavigator 42
BLAST 14 37—38 58—60 64 72—78 74f 101f
BLASTN 72
BLASTP 72
BLASTX 72
BLOCKS 115
Boolean logic 52
BOXSHADE 97
Branch-and-bound method 154—155
Brookhaven Protein Data Bank (PDB) 9
Canvas 123—124
Celera Genomics 13
CERN 32
CGC mapping tools, restriction mapping 121—123
CHIME 106
CHPmodels 112
Cinema 97
Cladistics 150 159
Clustal 92—93
CLUSTALW 94 125—126
Clustering algorithms 152—153
CN3D 106
COG (Clusters of Orthologous Groups) project 18
Coiled coil prediction 111
Coils 111
Comparative genomics 17—19
Compleat Cladist: A Primer of Phylogenetic Procedures 159
Computer software 175—180
Computer software, DNA sequencing 138—141
Computer software, Web integration 5—6
Computers 27—42
Computers, network 35—37
Computers, personal 34
Computers, research 33—34
CuraTools 6
DAS Transmembrane Prediction, Server 111
Databases, HTGS 66
Databases, integrated 8—9
Databases, laboratory 28—29
Databases, nucleotide sequence 76
Databases, peptide sequence 75—76
Databases, sequences, finding and retrieving 47—56
Databases, sequences, public 47—48
Databases, similarity searching 65—67
Databases, Web integration 5—6
Dayhoff, Margaret 63
DDBJ 66
Dendogram 150
Dense Alignment Surface (DAS), Transmembrane Prediction Server 111
desktop computers 28 34
Digitizer 134—135
Distance-based phylogeny methods 151—152
distances 156
DNA DataBank of Japan (DDBJ) 66
DNA Strider 123—124 124f
DNA, 3D model 99 100f
DNA, chips 16—17
DNA, chips, microarrays 11
DNA, distances 151
DNA, replication, controlled interruption 133
DNA, sequences, coding vs. noncoding 148—149
DNA, sequences, finding genes in 100—102
DNA, sequencing 133—144
DNA, sequencing, automated 11
DNA, sequencing, biochemistry 133—134
DNA, sequencing, computer software 138—141
DNA, sequencing, ordered subfragments 137
DNA, sequencing, primer walking 137
DNA, sequencing, shotgun 138
DNA, sequencing, software recommendations 140—144
DNA, sequencing, strategies 135—140
DNA, signal sequences 102—103
DNA, translation 102
DNS 31
DOE-NIH Human Genome Project 13
Domain Name System (DNS) 31
Dot plots 60—61
Double helix model 99 100f
Double Twist 5
Drosophila melanogaster 13
EMBL 29 66
Entrez 9 42 48—55
ENTREZ, cut and paste 52—55
ENTREZ, saving 55
ENTREZ, searching techniques 49—52
EPD 103
EST 11 14—15 66 100
EST, databanks 15
Ethernet 31
Eubacteria 18
Eukaryotae 18
Eukaryotic Promoter Database (EPD) 103
European Molecular Biology Laboratory (EMBL) 29 66
Evolution 145—146
Evolution, neutral theory of 148
ExPASy 9
expectation values 79
Expressed Sequence Tag (EST) 11 14—15 66 100
Expressed sequence tag (EST), databanks 15
False positives, BLAST 83f
FASTA 58—60 65 68—69 70f—71f
FASTA, format 69—72
FETCH 56
File Transfer Protocol (FTP) 48
FINDPATTERNS 103 116 123
FoldIt 106—107
FRAMESEARCH 80—82
Frameshifts 80—82
FreeHand 124
FTP 48
Gap 87
Gapped BLAST 73
GCG 5—6 38—42 56 140—143
gdb 8—9
GELASSEMBLE 142
GELDISASSEMBLE 142
GELENTER 142
GELMERGE 142
GELSTART 142
GELVIEW 142
GenBank 4 9 29 48
Gene Construction Kit 126—127 128f
| Gene duplication 146
GeneBee phylogenetics server 158
GeneExplorer 6
GeneFisher 131
Genes, finding in DNA sequences 100—102
GeneScape Portal 6
GeneStream server 89
Genetic drift 146
Genetic maps 8 23
Genetics 131
Genetics Computer Group (GCG) 5—6 38—42 56 140—143
GeneWorld 5—6
GenLang 102
Genome annotation problem 20—22
Genome bioinformatics 19—20
Genome Channel 21—22 22f
Genome Project 12—17 20—24
Genome Project, Internet 22—24
Genome Sequencing Center 15
Genome, sequence data, raw 14
Genome, sequences, Periodic Table of 20
Genome, sequencing 11—13
Genomic survey sequence (GSS) 66
Genomics 4 11—26
Genomics, comparative 17—19
Genomics, pharmaceutical research 24—26
GenPept 66 167
Global alignment vs. local alignment 59f 87—89
Goad, Walter 47
Grail 102
graphical user interfaces (GUIs) 33
GSS 66
Guex, Nicolas 106
GUIs 33
Helix-turn-helix motif prediction 111
Hennig, Willi 150
Heuristic programs, similarity searching 58—59
Hidden Markov Models (HMMs) 19
High-throughput genomic sequence (HTGS) databases 66
HMMER 117
HMMs 19
Homology searching 57
HTGS databases 66
Human Genome Database (GDB) 8 9
Human Genome Initiative 12
Human Genome Project, Information 13
Hydrophobicity plot 108
INCA 80
initn 68 168
Institute for Genomic Research (TIGR) 13
Integrated databases 8—9
Internet 3—4 29 see
Internet, genome project 22—24
Internet, growth 32—33
Internet, history 30—33
Introduction to Phylogenetic Systematics 159
Introduction to Some Computer Programs Used in Phylogenetics 159
Iterative Neighborhood Cluster Analysis (INCA) 80
Japanese International Protein, Information Database (JIPID) 67
Jesior, Jean-Claude 106—107
JIPID 67
Journey Into Phylogenetic Systematics 159
ktup value 68
Laboratory databases 28—29
LALIGN 87
Lander, Eric 20
LINEUP 96
Linnaeus 147 150
lookup 56
Los Alamos Sequence Database see "GenBank"
MACAW 92 96
MACCLADE 158
MacPattern 113
MacVector 93 125—126
Mainframes 35 37—38
MAP 89 121—122 122f
Mapping tools, restriction mapping 121—123
MAPPLOT 122
MAPSORT 122
Martinsried Institute for Protein Sequences (MIPS) 67
Maximum likelihood 155
Medline 29
Meme 117—118 117f
Microsatellites 140
Minisatellites 140
mips 19 67
Mosaic 32
Motifs 113
Motifs, new 116—118
MSA 89
MSF 90 90f
Multiple Alignment Construction and Analysis Workbench 92 96
Multiple alignments 85—97
Multiple alignments, editing and formatting 96—97
Multiple sequence alignment 89—95
Multiple sequence format (MSF) 90 90f
Munich Information Center for Protein Sequences (MIPS) 19
Mutation 148
National Center for Biotechnology Information (NCBI) 14
National Center for Supercomputing Applications 32
National Center or Human Genome Research (NCHGR) 12
National Human Genome Research Institute (NHGRI) 12
National Institute of General Medical Sciences (NIGMS) 47
NCBI 14
NCHGR 12
NCSA 32
Neighbor joining 153
NENTREZ 106
NETBLAST 37
NetBoot 36
Netscape 32
network computers 35—37
Network Protein Sequence Analysis (NPSA) 113
Neutral theory of evolution 148
NHGRI 12
NIGMS 47
NPSA 113
NRL_3D 67
NSFNET 31—32
Nucleotide sequence databases 76
Oak Ridge National Laboratory 21
Office for Human Genome Research 12
OMIGA 125—126 126f
Open reading frames (ORFs) 100—102
Ordered subfragments 137
ORFfinder 102
ORFs 100—102
OWL 67
Packet switching 31
Pairwise alignment 85—97
Pairwise alignment, servers 88—89
PAM 250 matrix 63—64
Parsimony 153—155 154f
PATCHX 67
PATMAT 113
Pattern matching 81—82
PAUP 156
PAUP/maximum likelihood package 155
PAUPSEARCH 156
PCR, primer design 129
PCR, primers 128
PDB 9 67 105—106
Pearson, William 68
PEDANT tool 19
Pedro's Biomolecular Research Tools 7
Peitsch, Manuel C. 106
Peptide (protein) sequence databases 75—76
PepTool 93 94f
Periodic Table of genomic sequences 20
personal computers 34
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