A Primer of Genome Sciences

by Gibson, Greg; Muse, Spencer V.

• ISBN13: 9780878932344
• ISBN10: 0878932348
• Format: Paperback
• Copyright: 2002-01-01
• Publisher: Sinauer Associates Inc

Summary

North Carolina State Univ., Raleigh. Introductory textbook for senior undergraduates or graduate students new to the field. Gives a background to the experimental methods, and and overview of what bioinformatics is about. Softcover.

Author Biography

Spencer Muse is Assistant Professor in the Department of Statistics, Bioinformatics Research Center at North Carolina State University.

Table of Contents

Preface	xi
Genome Projects: Organization and Objectives
The Core Aims of Genome Science	1	(3)
Mapping Genomes	4	(9)
Genetic Maps	4	(3)
Physical Maps	7	(1)
Cytological Maps	8	(2)
Comparative Genomics	10	(3)
The Human Genome Project	13	(13)
Objectives	13	(3)
The Content of the Human Genome	16	(2)
Ethical, Legal, and Social Implications of the Human Genome Project	18	(3)
Internet resources	21	(3)
Genbank Files	24	(2)
Animal Genome Projects	26	(11)
Mouse Genome Projects	26	(4)
Other Vertebrate Biomedical Models	30	(1)
Animal Breeding Projects	31	(1)
Invertebrate Model Organisms	32	(5)
Plant Genome Projects	37	(9)
Arabidopsis thaliana	37	(3)
Grasses and Legumes	40	(2)
Managing and Distrubuting Genome Data	42	(3)
Other Flowering Plants	45	(1)
Genome Projects	46	(11)
The Minimal Genome	46	(5)
Bacteria and Archaea	51	(2)
Yeast	53	(2)
Parasite Genomics	55	(2)
Summary Discussion Questions Literature Cited	57	(6)
Genome Sequencing and Annotation
Automated DNA Sequencing	63	(13)
The Principle of Sanger Sequencing	63	(1)
High-Throughput Sequencing	64	(2)
Reading Sequence Traces	66	(3)
Contig Assembly	69	(3)
Pairwise Sequence Alignment	72	(4)
Emerging Sequencing Methods	76	(2)
Genome Sequencing	78	(13)
Hierarchical Sequencing	78	(6)
Shotgun Sequencing	84	(2)
Searching Sequence Databases Using Blast	86	(4)
Sequence Verification	90	(1)
Genome Annotation	91	(14)
EST Sequencing	91	(2)
Ab initio Gene Discovery	93	(2)
Hidden Markov Models and Gene Finding	95	(3)
Non-Protein Coding Genes	98	(3)
Structural Features of Genome Sequences	101	(4)
Functional Annotation and Gene Family Clusters	105	(12)
Clustering of Genes by Sequence Similarity	106	(3)
Clusters of Orthologous Genes	109	(3)
Phylogenetic Classification of Genes	112	(1)
Gene Ontology	112	(2)
Phylogenetics	114	(3)
Summary Discussion Questions Web Site Exercises Literature Cited	117	(6)
Gene Expression and the Transcriptome
Parallel Analysis of Gene Expression: Microarrays	123	(24)
cDNA Microarray Technology	123	(7)
Microarray Image Processing	130	(2)
Statistical Analysis of cDNA Microarray Data and Experimental Design	132	(5)
Oligonucleotide Microarray Technology	137	(4)
Microarray Data Mining	141	(1)
Clustering Methods	142	(4)
Motif Detection in Promoter Sequences of Gene Clusters	146	(1)
SAGE, Microbeads, and Differential Display	147	(9)
Serial Analysis of Gene Expression	147	(5)
Microbead Technology	152	(3)
Differential Display	155	(1)
Single-Gene Analyses	156	(4)
Northern Blots and RNAse Protection	156	(2)
Quantitative PCR	158	(2)
Properties of Transcriptomes	160	(15)
Yeast	160	(5)
Cancer	165	(5)
Model Organisms	170	(3)
Gene Expression Databases	173	(2)
Summary Discussion Questions Web Site Exercises Literature Cited	175	(8)
Proteomics and Functional Genomics
Functional Proteomics	183	(21)
Protein Annotation	183	(3)
Hidden Markov Models in Domain Profiling	186	(2)
Protein Separation and 2D-Page	188	(5)
Mass Spectrometry and Protein Identification	193	(6)
Protein Microarrays	199	(3)
Protein Interaction Maps	202	(2)
Structural Proteomics	204	(8)
Objectives of Structural Proteomics	204	(3)
Protein Structure Determination	207	(3)
Protein Structure Prediction and Threading	210	(2)
Functional Genomics	212	(22)
Saturation Forward Genetics	213	(5)
High-Throughput Reverse Genetics	218	(4)
Transgenic Animals and Plants	222	(5)
Fine-Structure Genetics	227	(6)
Genetic Fingerprinting	233	(1)
Summary Discussion Questions Web Site Exercises Literature Cited	234	(7)
SNPs and Variation
The Nature of Single Nucleotide Polymorphisms	241	(11)
Classification	241	(3)
Distribution of SNPs	244	(4)
Disequilibrium between Alleles at Two Loci	248	(4)
Applications of SNP Technology	252	(19)
Population Genetics	252	(4)
Recombination Mapping	256	(2)
QTL Mapping	258	(3)
Linkage Disequilibrium Mapping	261	(5)
Case-Control Association Studies	266	(5)
SNP Discovery	271	(8)
Resequencing	271	(1)
Family-Based Association Tests	272	(5)
Sequence-Free Polymorphism Detection	277	(2)
SNP Genotyping	279	(13)
Low-Technology Methods	280	(2)
Hybridization-Based Methods	282	(2)
Minisequencing Methods	284	(4)
Homogeneous Fluorogenic Dye-Based Methods	288	(4)
Haplotype phasing methods	292	(1)
Summary Discussion Questions Web Site Exercises Literature Cited	292	(9)
Integrative Genomics
Metabolomics	301	(7)
Analysis of Cellular Constituents	301	(5)
Metabolic and Biochemical Databases	306	(2)
In silico Genomics	308	(9)
Metabolic Control Analysis	308	(5)
Systems-Level Modeling of Gene Networks	313	(4)
Summary Discussion Questions Literature Cited	317	(4)
Glossary	321	(12)
List of Abbreviations	333	(2)
Index	335