Verfügbarkeit: A primer of genome science

A primer of genome science:

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Bibliographische Detailangaben
1. Verfasser:	Gibson, Greg 1963- (VerfasserIn)
Format:	Buch
Sprache:	English
Veröffentlicht:	Sunderland, Mass. Sinauer 2004
Ausgabe:	2. ed.
Schlagworte:	Bioinformática Genomas Genomas - Investigaciones Genética Genexpression Genom Molekulare Bioinformatik Genanalyse
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	Includes bibliographical references and index
Beschreibung:	XIII, 378 S. Ill., graph. Darst.
ISBN:	0878932321

Internformat

MARC


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Datensatz im Suchindex

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adam_text	A PRIMER OF GENOME SCIENCE SECOND EDITION GREG GIBSON SPENCER V MUSE North Carolina State University SINAUER ASSOCIATES, INC PUBLISHERS Sunderland, Massachusetts, 01375 Contents Preface xi Genome Projects: Organization and Objectives The Core Aims of Genome Science Mapping Genomes 4 Genetic Maps 4 EXERCISE 1 1 Constructing a genetic map 7 Physical Maps 8 Cytological Maps 8 Comparative Genomics 10 The Human Genome Project 13 Objectives 13 The Content of the Human Genome 16 BOX 1 1 The Ethical, Legal, and Social Implica- tions of the Human Genome Project 18 Internet Resources 22 EXERCISE 1 2 Use the NCBI and Ensembl genome browsers to examine a human disease gene 23 Animal Genome Projects 25 BOX 1 2 GenBank Files 26 Rodent Genome Projects 29 EXERCISE 1 3 Compare the structure of a gene in a mouse and a human 32 Other Vertebrate Biomedical Models 33 Animal Breeding Projects 34 Invertebrate Model Organisms 35 BOX 1 3 Managing and Distributing Genome Data 38 Plant Genome Projects 41 Arabidopsis Thaliana 41 Grasses and Legumes 43 Other Flowering Plants 46 O Microbial Genome Projects 47 The Minimal Genome 47 Sequenced Microbial Genomes 51 EXERCISE 1 4 Compare two microbial genomes using the CMR 52 Environmental Sequencing 53 Yeast 55 EXERCISE 1 5 Examining a gene in the Saccha- romyces Genome Database 56 Parasite Genomics 57 Summary • Discussion Questions • Literature Cited 59 Genome Sequencing and Annotation Automated DNA Sequencing 65 The Principle ofSanger Sequencing 65 High-Throughput Sequencing 66 Reading Sequence Traces 68 EXERCISE 2 1 Reading a sequence trace 71 Contig Assembly 72 BOX 2 1 Pairwise Sequence Alignment 74 EXERCISE 2 2 Computing an optimal sequence alignment 78 Emerging Sequencing Methods 79 Genome Sequencing 81 Hierarchical Sequencing 82 Shotgun Sequencing 86 BOX 2 2 Searching Sequence Databases Using BLAST 88 Sequence Verification 92 GENOME ANNOTATION 93 EST Sequencing 93 Ab Initio Gene Discovery 96 3 SNPs and Variation The Nature of Single Nucleotide Polymorphisms 133 Classification of SNPs 133, • Distribution of SNPs 13 6 Linkage Disequilibrium and Haplotype Maps 138 BOX 3 1 Disequilibrium between Alleles at Two Loci 140 EXERCISE 3 1 Quantifying heterozygosity and ID 143 Applications of SNP Technology 147 Population Genetics 147 BOX 3 2 The Coalescent 150 Recombination Mapping 153 EXERCISE 3 2 Inferring haplotype structure 154 QTL Mapping 156 Linkage Disequilibrium Mapping 159 BOX 3 3 Case-Control Association Studies 164 BOX 2 3 Hidden Markov Models and Gene Finding 97 Regulatory Sequences 101 Non-Protein Coding Genes 102 Structural Features of Genome Sequences Functional Annotation and Gene Family Clusters 110 EXERCISE 2 3 Perform a BLAST search 111 Clustering of Genes by Sequence Similarity 112 Clusters of Orthologous Genes 114 Phylogenetic Classification of Genes 115 BOX 2 4 Phylogenetics 116 EXERCISE 24A simple phylogenetic analysis 120 Gene Ontology 122 BOX 2 5 Gene Ontologies 124 Summary • Discussion Questions • Web Site Exercises • Literature Cited 126 O BOX 3 4 Family-Based Association Tests 168 EXERCISE 3 3 Perform a case-control association test 171 SNP Discovery 172 Resequencing 172 Sequence-Free Polymorphism Detection 174 SNP Genotyping 176 Low-Technology Methods 178 Minisequencing Methods 178 EXERCISE 3 4 Designing a genotyping assay for a double polymorphism 184 Homogeneous Fluorogenic Dye-Based Methods 184 Haplotype Phasing Methods 188 Summary • Discussion Questions • Web Site Exercises • Literature Cited 188 Gene Expression and the Transcriptome Parallel Analysis of Gene Expression: Microarrays 195 Applications of M icroarray Technology 196 Experimental Design 198 EXERCISE 4 1 Design a microarray experiment 200 Microarray Technologies 202 Statistical Analysis ofcDNA Microarray Data 211 BOX 4 1 Microarray Image Processing 214 EXERCISE 4 2 Calculate which genes are differentially expressed 216 BOX 4 2 Basic Statistical Methods 220 EXERCISE 4 3 Evaluate the significance of the following gene expression differences 223 Microarray Data Mining 224 BOX 4 3 Clustering Methods 226 EXERCISE 4 4 Perform a cluster analysis on gene expression profiles 229 ChIP Chips and Gene Regulation 230 SAGE and Microbeads 232 Serial Analysis of Gene Expression 232 BOX 4 4 Motif Detection in Promoter Sequences 234 Microbead-Based Expression Profiling 239 Single-Gene Analyses 239 Northern Blots 239 Quantitative PCR 241 Properties of Transcriptomes 242 Microbial Transcriptomics 243 Cancer and Clinical Applications 247 Development, Physiology, and Behavior 250 Evolutionary and Ecological Functional Genomics 253 Gene Expression Databases 255 Summary • Discussion Questions • Web Site Exercises • Literature Cited 258 5 QProteomics and Functional Genomics Functional Proteomics 265 Protein Annotation 265 EXERCISE 5 1 Structural annotation of a protein 268 BOX 5 1 Hidden Markov Models in Domain Profiling 270 Prptein Separation and 2D-PAGE 273 Mass Spectrometry and Protein Identification 277 EXERCISE 5 2 Identification of a protein on the basis of a MS profile 280 Protein Microarrays 283 Protein Interaction Maps 285 EXERCISE 5 3 Formulating a network of protein interactions 287 Structural Proteomics 289 Objectives of Structural Proteomics 289 BOX 5 2 Biological Networks In Genome Science 290 Protein Structure Determination 294 Protein Structure Prediction and Threading Functional Genomics 300 Saturation Forward Genetics 301 High-Throughput Reverse Genetics 306 BOX 5 3 Transgenic Animals and Plants 312 Fine-Structure Genetics 314 EXERCISE 5 4 Designing a genetic screen 316 Genetic Fingerprinting 321 Summary • Discussion Questions • Web Site Exercises • Literature Cited 322
adam_txt	A PRIMER OF GENOME SCIENCE SECOND EDITION GREG GIBSON SPENCER V MUSE North Carolina State University SINAUER ASSOCIATES, INC PUBLISHERS Sunderland, Massachusetts, 01375 Contents Preface xi Genome Projects: Organization and Objectives The Core Aims of Genome Science Mapping Genomes 4 Genetic Maps 4 EXERCISE 1 1 Constructing a genetic map 7 Physical Maps 8 Cytological Maps 8 Comparative Genomics 10 The Human Genome Project 13 Objectives 13 The Content of the Human Genome 16 BOX 1 1 The Ethical, Legal, and Social Implica- tions of the Human Genome Project 18 Internet Resources 22 EXERCISE 1 2 Use the NCBI and Ensembl genome browsers to examine a human disease gene 23 Animal Genome Projects 25 BOX 1 2 GenBank Files 26 Rodent Genome Projects 29 EXERCISE 1 3 Compare the structure of a gene in a mouse and a human 32 Other Vertebrate Biomedical Models 33 Animal Breeding Projects 34 Invertebrate Model Organisms 35 BOX 1 3 Managing and Distributing Genome Data 38 Plant Genome Projects 41 Arabidopsis Thaliana 41 Grasses and Legumes 43 Other Flowering Plants 46 O Microbial Genome Projects 47 The Minimal Genome 47 Sequenced Microbial Genomes 51 EXERCISE 1 4 Compare two microbial genomes using the CMR 52 Environmental Sequencing 53 Yeast 55 EXERCISE 1 5 Examining a gene in the Saccha- romyces Genome Database 56 Parasite Genomics 57 Summary • Discussion Questions • Literature Cited 59 Genome Sequencing and Annotation Automated DNA Sequencing 65 The Principle ofSanger Sequencing 65 High-Throughput Sequencing 66 Reading Sequence Traces 68 EXERCISE 2 1 Reading a sequence trace 71 Contig Assembly 72 BOX 2 1 Pairwise Sequence Alignment 74 EXERCISE 2 2 Computing an optimal sequence alignment 78 Emerging Sequencing Methods 79 Genome Sequencing 81 Hierarchical Sequencing 82 Shotgun Sequencing 86 BOX 2 2 Searching Sequence Databases Using BLAST 88 Sequence Verification 92 GENOME ANNOTATION 93 EST Sequencing 93 Ab Initio Gene Discovery 96 3 SNPs and Variation The Nature of Single Nucleotide Polymorphisms 133 Classification of SNPs 133, • Distribution of SNPs 13'6 Linkage Disequilibrium and Haplotype Maps 138 BOX 3 1 Disequilibrium between Alleles at Two Loci 140 EXERCISE 3 1 Quantifying heterozygosity and ID 143 Applications of SNP Technology 147 Population Genetics 147 BOX 3 2 The Coalescent 150 Recombination Mapping 153 EXERCISE 3 2 Inferring haplotype structure 154 QTL Mapping 156 Linkage Disequilibrium Mapping 159 BOX 3 3 Case-Control Association Studies 164 BOX 2 3 Hidden Markov Models and Gene Finding 97 Regulatory Sequences 101 Non-Protein Coding Genes 102 Structural Features of Genome Sequences Functional Annotation and Gene Family Clusters 110 EXERCISE 2 3 Perform a BLAST search 111 Clustering of Genes by Sequence Similarity 112 Clusters of Orthologous Genes 114 Phylogenetic Classification of Genes 115 BOX 2 4 Phylogenetics 116 EXERCISE 24A simple phylogenetic analysis 120 Gene Ontology 122 BOX 2 5 Gene Ontologies 124 Summary • Discussion Questions • Web Site Exercises • Literature Cited 126 O BOX 3 4 Family-Based Association Tests 168 EXERCISE 3 3 Perform a case-control association test 171 SNP Discovery 172 Resequencing 172 Sequence-Free Polymorphism Detection 174 SNP Genotyping 176 Low-Technology Methods 178 Minisequencing Methods 178 EXERCISE 3 4 Designing a genotyping assay for a double polymorphism 184 Homogeneous Fluorogenic Dye-Based Methods 184 Haplotype Phasing Methods 188 Summary • Discussion Questions • Web Site Exercises • Literature Cited 188 Gene Expression and the Transcriptome Parallel Analysis of Gene Expression: Microarrays 195 Applications of M icroarray Technology 196 Experimental Design 198 EXERCISE 4 1 Design a microarray experiment 200 Microarray Technologies 202 Statistical Analysis ofcDNA Microarray Data 211 BOX 4 1 Microarray Image Processing 214 EXERCISE 4 2 Calculate which genes are differentially expressed 216 BOX 4 2 Basic Statistical Methods 220 EXERCISE 4 3 Evaluate the significance of the following gene expression differences 223 Microarray Data Mining 224 BOX 4 3 Clustering Methods 226 EXERCISE 4 4 Perform a cluster analysis on gene expression profiles 229 ChIP Chips and Gene Regulation 230 SAGE and Microbeads 232 Serial Analysis of Gene Expression 232 BOX 4 4 Motif Detection in Promoter Sequences 234 Microbead-Based Expression Profiling 239 Single-Gene Analyses 239 Northern Blots 239 Quantitative PCR 241 Properties of Transcriptomes 242 Microbial Transcriptomics 243 Cancer and Clinical Applications 247 Development, Physiology, and Behavior 250 Evolutionary and Ecological Functional Genomics 253 Gene Expression Databases 255 Summary • Discussion Questions • Web Site Exercises • Literature Cited 258 5 QProteomics and Functional Genomics Functional Proteomics 265 Protein Annotation 265 EXERCISE 5 1 Structural annotation of a protein 268 BOX 5 1 Hidden Markov Models in Domain Profiling 270 Prptein Separation and 2D-PAGE 273 Mass Spectrometry and Protein Identification 277 EXERCISE 5 2 Identification of a protein on the basis of a MS profile 280 Protein Microarrays 283 Protein Interaction Maps 285 EXERCISE 5 3 Formulating a network of protein interactions 287 Structural Proteomics 289 Objectives of Structural Proteomics 289 BOX 5 2 Biological Networks In Genome Science 290 Protein Structure Determination 294 Protein Structure Prediction and Threading Functional Genomics 300 Saturation Forward Genetics 301 High-Throughput Reverse Genetics 306 BOX 5 3 Transgenic Animals and Plants 312 Fine-Structure Genetics 314 EXERCISE 5 4 Designing a genetic screen 316 Genetic Fingerprinting 321 Summary • Discussion Questions • Web Site Exercises • Literature Cited 322
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subject_GND	(DE-588)4020136-3 (DE-588)4156640-3 (DE-588)4531334-9 (DE-588)4200230-8
title	A primer of genome science
title_auth	A primer of genome science
title_exact_search	A primer of genome science
title_exact_search_txtP	A primer of genome science
title_full	A primer of genome science Greg Gibson ; Spencer V. Muse
title_fullStr	A primer of genome science Greg Gibson ; Spencer V. Muse
title_full_unstemmed	A primer of genome science Greg Gibson ; Spencer V. Muse
title_short	A primer of genome science
title_sort	a primer of genome science
topic	Bioinformática Genomas Genomas - Investigaciones Genética Genexpression (DE-588)4020136-3 gnd Genom (DE-588)4156640-3 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd Genanalyse (DE-588)4200230-8 gnd
topic_facet	Bioinformática Genomas Genomas - Investigaciones Genética Genexpression Genom Molekulare Bioinformatik Genanalyse
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014638807&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
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