Principles of Genome Analysis and Genomics (Third Edition)

Contents......Page 4
Preface......Page 6
Abbreviations......Page 7
Physical mapping of genomes......Page 10
Sequencing whole genomes......Page 12
Benefits of genome sequencing
......Page 14
Outline of the rest of the book......Page 15
Suggested reading......Page 17
Useful websites......Page 18
Genome size......Page 19
Sequence complexity......Page 20
Introns and exons......Page 22
Genome structure in viruses and prokaryotes......Page 25
The organization of organelle genomes......Page 27
The organization of nuclear DNA in eukaryotes......Page 28
Useful websites......Page 42
Fragmentation of DNA with restriction enzymes......Page 43
Separating large fragments of DNA......Page 45
Isolation of chromosomes......Page 46
Vectors for cloning DNA......Page 48
Yeast artificial chromosomes......Page 49
P1-derived and bacterial artificial chromosomes as alternatives to yeast artificial chromosomes
......Page 51
Retrofitting......Page 53
Suggested reading......Page 54
Useful website......Page 55
Restriction enzyme fingerprinting......Page 56
Marker sequences......Page 58
Hybridization assays......Page 68
Physical mapping without cloning......Page 73
Integration of different mapping methods......Page 78
Useful websites......Page 79
Basic DNA sequencing......Page 80
Modifications of chain-terminator sequencing......Page 82
Automated DNA sequencing......Page 84
DNA sequencing by capillary array electrophoresis......Page 85
High throughput sequencing......Page 86
Sequencing strategies......Page 87
Alternative DNA sequencing methodologies......Page 94
Suggested reading......Page 101
Useful websites......Page 102
Traditional routes to gene identification......Page 103
Overview of sequence analysis......Page 106
Software programs for finding genes......Page 108
Using homology to find genes......Page 111
Identifying the function of a new gene......Page 114
Secondary databases of functional domains......Page 116
Analyses not based on homology......Page 117
Molecular phylogenetics......Page 120
Useful websites......Page 121
Protein evolution by exon shuffling
......Page 122
Comparative genomics of prokaryotes......Page 123
Comparative genomics of organelles......Page 130
Comparative genomics of eukaryotes......Page 132
Other aspects of comparative genomics......Page 139
Useful websites......Page 141
Determining gene function by sequence comparison......Page 142
Determining gene function through conserved protein structure......Page 143
Approaches to protein structural genomics......Page 145
Suggested reading......Page 153
Useful website......Page 154
Traditional approaches to expression profiling......Page 155
Global analysis of RNA expression......Page 157
Global analysis of protein expression......Page 172
Suggested reading......Page 180
Useful websites......Page 181
High-throughput systematic gene knockout......Page 182
Genome-wide random mutagenesis......Page 184
Useful websites......Page 195
Methods for protein interaction analysis......Page 196
Library-based methods for screening protein interactions......Page 198
Informatics tools and resources for protein interaction data......Page 205
Useful websites......Page 208
Theme 1:Understanding genetic diseases of humans......Page 209
Theme 2:Understanding responses to drugs (pharmacogenomics)......Page 218
Theme 3:Understanding and combatting bacterial pathogenicity......Page 220
Theme 4:Getting to grips with quantitative traits......Page 227
Theme 5:The impact of genomics on agriculture......Page 232
Theme 6:Developmental genomics......Page 234
Suggested reading......Page 237
References......Page 239
Index......Page 264