Pub. Date:
Sinauer Associates, Incorporated
Primer in Genome Sciences / Edition 1

Primer in Genome Sciences / Edition 1


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A textbook for an introduction to genome science for senior undergraduates or graduates who are new to the field. Gibson and Muse decided that the field has now stabilized enough that fundamental principles of theory and experimental methods can be learned that will continue to inform new studies in biomedical and agricultural research for the next several years. They assume students have completed an upper level undergraduate course in genetics. The glossary does not indicate pronunciation. Annotation c. Book News, Inc., Portland, OR (

Product Details

ISBN-13: 9780878932344
Publisher: Sinauer Associates, Incorporated
Publication date: 01/15/2002
Edition description: Older Edition
Pages: 347
Product dimensions: 6.30(w) x 9.06(h) x (d)

Table of Contents

1Genome Projects: Organization and Objectives
The Core Aims of Genome Science1
Mapping Genomes4
Genetic Maps4
Physical Maps7
Cytological Maps8
Comparative Genomics10
The Human Genome Project13
The Content of the Human Genome16
Internet resources21
Animal Genome Projects26
Mouse Genome Projects26
Other Vertebrate Biomedical Models30
Animal Breeding Projects31
Invertebrate Model Organisms32
Plant Genome Projects37
Arabidopsis thaliana37
Grasses and Legumes40
Other Flowering Plants45
Genome Projects46
The Minimal Genome46
Bacteria and Archaea51
Parasite Genomics55
Discussion Questions
Literature Cited
2Genome Sequencing and Annotation
Automated DNA Sequencing63
The Principle of Sanger Sequencing63
High-Throughput Sequencing64
Reading Sequence Traces66
Contig Assembly69
Emerging Sequencing Methods76
Genome Sequencing78
Hierarchical Sequencing78
Shotgun Sequencing84
Sequence Verification90
Genome Annotation91
EST Sequencing91
Ab initio Gene Discovery93
Non-Protein Coding Genes98
Structural Features of Genome Sequences101
Functional Annotation and Gene Family Clusters105
Clustering of Genes by Sequence Similarity106
Clusters of Orthologous Genes109
Phylogenetic Classification of Genes112
Gene Ontology112
Discussion Questions
Web Site Exercises
Literature Cited
3Gene Expression and the Transcriptome
Parallel Analysis of Gene Expression: Microarrays123
cDNA Microarray Technology123
Statistical Analysis of cDNA Microarray Data and Experimental Design132
Oligonucleotide Microarray Technology137
Microarray Data Mining141
SAGE, Microbeads, and Differential Display147
Serial Analysis of Gene Expression147
Microbead Technology152
Differential Display155
Single-Gene Analyses156
Northern Blots and RNAse Protection156
Quantitative PCR158
Properties of Transcriptomes160
Model Organisms170
Gene Expression Databases173
Discussion Questions
Web Site Exercises
Literature Cited
4Proteomics and Functional Genomics
Functional Proteomics183
Protein Annotation183
Protein Separation and 2D-PAGE188
Mass Spectrometry and Protein Identification193
Protein Microarrays199
Protein Interaction Maps202
Structural Proteomics204
Objectives of Structural Proteomics204
Protein Structure Determination207
Protein Structure Prediction and Threading210
Functional Genomics212
Saturation Forward Genetics213
High-Throughput Reverse Genetics218
Fine-Structure Genetics227
Genetic Fingerprinting233
Discussion Questions
Web Site Exercises
Literature Cited
5SNPs and Variation
The Nature of Single Nucleotide Polymorphisms241
Distribution of SNPs244
Applications of SNP Technology252
Population Genetics252
Recombination Mapping256
QTL Mapping258
Linkage Disequilibrium Mapping261
SNP Discovery271
Sequence-Free Polymorphism Detection277
SNP Genotyping279
Low-Technology Methods280
Hybridization-Based Methods282
Minisequencing Methods284
Homogeneous Fluorogenic Dye-Based Methods288
Haplotype phasing methods292
Discussion Questions
Web Site Exercises
Literature Cited
6Integrative Genomics
Analysis of Cellular Constituents301
Metabolic and Biochemical Databases306
In silico Genomics308
Metabolic Control Analysis308
Systems-Level Modeling of Gene Networks313
Discussion Questions
Literature Cited
List of Abbreviations333

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