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| Brown S.M. — Bioinformatics: A Biologist's Guide to Biocomputing and the Internet |
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| Предметный указатель |
Pfam 115
PFTOOLS 117
Pharmaceutical research genomics 24—25
Phenetics 150
Phrap 144
PHRED 143—144
PHYLIP 156—157 159
PHYLIP, server 158
Phylodendron 158
Phylogenetic analysis using parsimony (PAUP)/maximum likelihood package 155
Phylogenetic trees 146f
Phylogenetic trees, cladistic vs. phenetic analysis 150—155
Phylogenetic treesclustering algorithms 152—153
Phylogenetic treescomputer software 155—158
Phylogenetics, analysis 159
Phylogenetics, taxonomy 145—149
Phylogenetics, World Wide Web 158—159
Phylogeny, distance-based 151—152
Pileup 75 89—91 91f 96—97 152—153
Pima 89
PIR 29 67
Plasmid mapping 121—132
PLASMIDMAP 123
Polymerase chain reaction (PCR), primer design 129
Polymerase chain reaction (PCR), primers 128
Polymorphisms 15—16
Position Specific Iterated-BLAST (PSI-BLAST) 73 75
PPSRCH 114
PREDATOR 110—111
PredictProtein 111 112
PRETTY 96—97
PRETTYBOX 96
Prime 130
PRIME3 130
Primer design, programs 129—132
Primer walking 137
Primers! 130—132
prints 115
ProDom 115 116f
PROFILESEARCH 75
Promoter Scan 103
Promoter Scan II 103
PROSITE 9 113 114f 115
PROSITE ProfileScan 115
Protein Data Bank 67
Protein Data Base (PDB) 105—106
Protein extraction description and analysis (PEDANT) tool 19
Protein Fold Recognition Server 111 112
Protein Hydrophobicity Server 108
Protein Information Resource (PIR) 29 67
Proteins, composition 108—112
Proteins, distances 151—152
Proteins, function, prediction 99—100
Proteins, motifs 113—114
Proteins, profiles 114—116
Proteins, secondary structure 108—112
Proteins, sequence databases 75—76
Proteins, sequences 105
Proteins, sequences, divergence 146—147
Proteins, similarity searching, tips 78—79
Proteins, structure 104—108 107f
Proteins, structure-function 99—100
Proteins, super-secondary structure 111—112
Proteins, tertiary structure 112
PSI-BLAST 73 75
PSINET 32
Public databases sequences 47—48
PubMed 9
RASMOL 106
Recombination 146—147
Research, computers 33—34
Research, scaling up 3
Restriction mapping 121—123
Restriction mapping, CGC mapping tools 121—123
RNA structure 103—104 104f
Saccharomyces Genome Database (SGD) 8—9
Sanger Centre 14
Sanger method 133
SAPS 108
SBASE 115
SBDS 89
ScanProsite 113
scop 115
Search TransFac 103
Secondary Structural Content Prediction (SSCP) 110
SEQED 142
| SeqLab 91
Sequence comparison 60—61
Sequence data 4
Sequence homology 173
Sequence Retrieval System (SRS) 55—56
Sequence similarity 57—60
Sequence similarity, distances 61—64
Sequence similarity, dot plots 60—61
Sequence tagged sites (STSs) 66
Sequencer 139 140f 142—144 143f
Sequencers, automated 135
Sequences, DNA, coding vs. noncoding 148—149
Sequences, DNA, finding genes in 100—102
Sequences, finding and retrieving 47—56
Seqweb 6 41—42
SGD 8—9
Shotgun sequencing 138
Signal Scan 103
SignalP 112
Similarity score 58
Similarity searching 57—83
Similarity searching output interpretation 82—83
Similarity searching, databases 65—67
Similarity searching, heuristic programs 58—59
Similarity searching, tips 78—80
Similarity searching, World Wide Web 64
Similarity tools 58
Smith — Waterman algorithm 58 65
Software 175—180
Software, DNA sequencing 138—141
Software, Web integration 5—6
SOSUI 111
Southampton Bioinformatics Data Server (SBDS) 89
SPRED 109
SRS 55—56
SSCP 110
Staden, Roger 39
Statistical analysis of protein sequences 108
Stride 109
STS 66
SWISS-2DPAGE 9
SWISS-3DIMAGE 9
Swiss-PDB Viewer 106
Swiss-Prot 9 29 66
SwissModel 112
Systematics 147
Tandem repeats 140
TargetFinder 103
Taxonomy, phylogenetics 145—149
TBLASTN 72
TBLASTX 72
TCP/IP 31
Tertiary structure, prediction 105
TESS 103
TFASTX 80—82
TFDATA 103
TIGR 13
TMpred 111
Tomlinson, Ray 31
ToPLign 89
Transcription Element Search, Software 103
TRANSFAC 102—103
Transmission Control Protocol/Internet Protocol (TCP/IP) 31
Tree of Life Project 159
TREMBL 66—67
Twilight zone proteins 79—80
Unfinished genomes, Web sites 14
Unweighted pair group method algorithm (UPGMA), arithmetic averages 152—153
USENET 31 35—36
UUNet 32
Vector NTI 7 29 127—129 128f
Venter, Craig 13
Watson, James D. 12
Web 5—6
Web, Phylogenetics 158—159
Web, similarity searches 64
What is There (WIT) 19
Wisconsin Package Interface (WPI) 40—41
Wisconsin Sequence Analysis Package 5—6
WIT 19
Workstation 35
World Wide Web 5—6
World Wide Web, Phylogenetics 158—159
World Wide Web, similarity searches 64
WPI 40—41
XALIGN 93
Xprimer 131
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